set dir = $cwd
-set VER = 4.5
+set VER = 4.6
set MANDIR = online
set HTML = $cwd/html
set HTMLOL = $HTML/$MANDIR
<td ALIGN=LEFT VALIGN=TOP WIDTH=280>
<br><br>
<h2>
-GROMACS 4.5<br>
+GROMACS 4.6<br>
Online Reference</h2>
</td>
</TABLE></TD>
<td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
-<B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td>
+<B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td>
</tr>
</table>
<br>
EOD
foreach program ( $PROGRAMS )
- if ( ( -x $GMXBINDIR/$program ) && ( $program != "my_dssp" ) && ( $program != "GMXRC" ) && ( $program != "completion.csh" ) && ( $program != "completion.zsh" ) && ( $program != "average" ) && ( $program != "completion.bash" ) && ( $program != "luck" ) ) then
+ if ( ( -x $GMXBINDIR/$program ) && ( $program != "my_dssp" ) && ( $program != "GMXRC" ) && ( $program != "completion.csh" ) && ( $program != "completion.zsh" ) && ( $program != "average" ) && ( $program != "completion.bash" ) && ( $program != "luck" ) && ( $program != "demux.pl" ) && ( $program != "xplor2gmx.pl" ) ) then
echo "<br><a href="$MANDIR/$program.html">$program</a>" >> $HTMLIDX
endif
end
<HTML>
<HEAD>
-<TITLE>GROMACS 4.5 Online Reference </TITLE>
+<TITLE>GROMACS 4.6 Online Reference </TITLE>
</HEAD>
<LINK rel=stylesheet href="online/style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<td ALIGN=LEFT VALIGN=TOP WIDTH=280>
<br><br>
<h2>
-GROMACS 4.5<br>
+GROMACS 4.6<br>
Online Reference</h2>
</td>
</TABLE></TD>
<td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
-<B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td>
+<B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td>
</tr>
</table>
<multicol cols=5>
<A HREF="online/options.html">Options</a>
<br>
-<br><a href=online/demux.pl.html>demux.pl</a>
<br><a href=online/do_dssp.html>do_dssp</a>
<br><a href=online/editconf.html>editconf</a>
<br><a href=online/eneconv.html>eneconv</a>
<br><a href=online/g_current.html>g_current</a>
<br><a href=online/g_density.html>g_density</a>
<br><a href=online/g_densmap.html>g_densmap</a>
+<br><a href=online/g_densorder.html>g_densorder</a>
<br><a href=online/g_dielectric.html>g_dielectric</a>
+<br><a href=online/g_dih.html>g_dih</a>
<br><a href=online/g_dipoles.html>g_dipoles</a>
<br><a href=online/g_disre.html>g_disre</a>
<br><a href=online/g_dist.html>g_dist</a>
+<br><a href=online/g_dos.html>g_dos</a>
+<br><a href=online/g_dyecoupl.html>g_dyecoupl</a>
<br><a href=online/g_dyndom.html>g_dyndom</a>
+<br><a href=online/genbox.html>genbox</a>
+<br><a href=online/genconf.html>genconf</a>
<br><a href=online/g_enemat.html>g_enemat</a>
<br><a href=online/g_energy.html>g_energy</a>
+<br><a href=online/genion.html>genion</a>
+<br><a href=online/genrestr.html>genrestr</a>
<br><a href=online/g_filter.html>g_filter</a>
<br><a href=online/g_gyrate.html>g_gyrate</a>
<br><a href=online/g_h2order.html>g_h2order</a>
<br><a href=online/g_hbond.html>g_hbond</a>
<br><a href=online/g_helix.html>g_helix</a>
<br><a href=online/g_helixorient.html>g_helixorient</a>
+<br><a href=online/g_hydorder.html>g_hydorder</a>
+<br><a href=online/g_kinetics.html>g_kinetics</a>
<br><a href=online/g_lie.html>g_lie</a>
<br><a href=online/g_luck.html>g_luck</a>
<br><a href=online/g_mdmat.html>g_mdmat</a>
<br><a href=online/g_mindist.html>g_mindist</a>
<br><a href=online/g_morph.html>g_morph</a>
<br><a href=online/g_msd.html>g_msd</a>
+<br><a href=online/gmxcheck.html>gmxcheck</a>
+<br><a href=online/gmxdump.html>gmxdump</a>
<br><a href=online/g_nmeig.html>g_nmeig</a>
<br><a href=online/g_nmens.html>g_nmens</a>
<br><a href=online/g_nmtraj.html>g_nmtraj</a>
+<br><a href=online/g_options.html>g_options</a>
<br><a href=online/g_order.html>g_order</a>
+<br><a href=online/g_pme_error.html>g_pme_error</a>
<br><a href=online/g_polystat.html>g_polystat</a>
<br><a href=online/g_potential.html>g_potential</a>
<br><a href=online/g_principal.html>g_principal</a>
<br><a href=online/g_rms.html>g_rms</a>
<br><a href=online/g_rmsdist.html>g_rmsdist</a>
<br><a href=online/g_rmsf.html>g_rmsf</a>
+<br><a href=online/grompp.html>grompp</a>
<br><a href=online/g_rotacf.html>g_rotacf</a>
<br><a href=online/g_rotmat.html>g_rotmat</a>
<br><a href=online/g_saltbr.html>g_saltbr</a>
+<br><a href=online/g_sans.html>g_sans</a>
<br><a href=online/g_sas.html>g_sas</a>
<br><a href=online/g_select.html>g_select</a>
<br><a href=online/g_sgangle.html>g_sgangle</a>
<br><a href=online/g_wham.html>g_wham</a>
<br><a href=online/g_wheel.html>g_wheel</a>
<br><a href=online/g_x2top.html>g_x2top</a>
-<br><a href=online/g_xrama.html>g_xrama</a>
-<br><a href=online/genbox.html>genbox</a>
-<br><a href=online/genconf.html>genconf</a>
-<br><a href=online/genion.html>genion</a>
-<br><a href=online/genrestr.html>genrestr</a>
-<br><a href=online/gmxcheck.html>gmxcheck</a>
-<br><a href=online/gmxdump.html>gmxdump</a>
-<br><a href=online/grompp.html>grompp</a>
<br><a href=online/make_edi.html>make_edi</a>
<br><a href=online/make_ndx.html>make_ndx</a>
<br><a href=online/mdrun.html>mdrun</a>
<br><a href=online/mk_angndx.html>mk_angndx</a>
-<br><a href=online/ngmx.html>ngmx</a>
<br><a href=online/pdb2gmx.html>pdb2gmx</a>
<br><a href=online/tpbconv.html>tpbconv</a>
<br><a href=online/trjcat.html>trjcat</a>
<br><a href=online/trjconv.html>trjconv</a>
<br><a href=online/trjorder.html>trjorder</a>
-<br><a href=online/xplor2gmx.pl.html>xplor2gmx.pl</a>
<br><a href=online/xpm2ps.html>xpm2ps</a>
</multicol>
</TD>
<A HREF="#HNR11">Structural properties</A><br>
<A HREF="#HNR12">Kinetic properties</A><br>
<A HREF="#HNR13">Electrostatic properties</A><br>
-<A HREF="#HNR14">Protein specific analysis</A><br>
+<A HREF="#HNR14">Protein-specific analysis</A><br>
<A HREF="#HNR15">Interfaces</A><br>
<A HREF="#HNR16">Covariance analysis</A><br>
<A HREF="#HNR17">Normal modes</A><br>
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Generating topologies and coordinates</b>
-<TR><TD><A HREF="online/pdb2gmx.html">pdb2gmx</A></TD><TD>converts pdb files to topology and coordinate files</TD>
-<TR><TD><A HREF="online/g_x2top.html">g_x2top</A></TD><TD>generates a primitive topology from coordinates </TD>
<TR><TD><A HREF="online/editconf.html">editconf</A></TD><TD>edits the box and writes subgroups </TD>
+<TR><TD><A HREF="online/g_protonate.html">g_protonate</A></TD><TD>protonates structures</TD>
+<TR><TD><A HREF="online/g_x2top.html">g_x2top</A></TD><TD>generates a primitive topology from coordinates </TD>
<TR><TD><A HREF="online/genbox.html">genbox</A></TD><TD>solvates a system</TD>
-<TR><TD><A HREF="online/genion.html">genion</A></TD><TD>generates mono atomic ions on energetically favorable positions</TD>
<TR><TD><A HREF="online/genconf.html">genconf</A></TD><TD>multiplies a conformation in 'random' orientations</TD>
+<TR><TD><A HREF="online/genion.html">genion</A></TD><TD>generates mono atomic ions on energetically favorable positions</TD>
<TR><TD><A HREF="online/genrestr.html">genrestr</A></TD><TD>generates position restraints or distance restraints for index groups</TD>
-<TR><TD><A HREF="online/g_protonate.html">g_protonate</A></TD><TD>protonates structures</TD>
+<TR><TD><A HREF="online/pdb2gmx.html">pdb2gmx</A></TD><TD>converts coordinate files to topology and FF-compliant coordinate files</TD>
</TABLE>
<A NAME="HNR2">
<TR><TD>
<TR><TD COLSPAN=2><b>Running a simulation</b>
<TR><TD><A HREF="online/grompp.html">grompp</A></TD><TD>makes a run input file</TD>
-<TR><TD><A HREF="online/tpbconv.html">tpbconv</A></TD><TD>makes a run input file for restarting a crashed run</TD>
<TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>performs a simulation, do a normal mode analysis or an energy minimization</TD>
+<TR><TD><A HREF="online/tpbconv.html">tpbconv</A></TD><TD>makes a run input file for restarting a crashed run</TD>
</TABLE>
<A NAME="HNR3">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Viewing trajectories</b>
-<TR><TD><A HREF="online/ngmx.html">ngmx</A></TD><TD>displays a trajectory</TD>
-<TR><TD><A HREF="online/g_highway.html">g_highway</A></TD><TD>X Window System gadget for highway simulations</TD>
<TR><TD><A HREF="online/g_nmtraj.html">g_nmtraj</A></TD><TD>generate a virtual trajectory from an eigenvector</TD>
+<TR><TD><A HREF="online/ngmx.html">ngmx</A></TD><TD>displays a trajectory</TD>
</TABLE>
<A NAME="HNR4">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Processing energies</b>
-<TR><TD><A HREF="online/g_energy.html">g_energy</A></TD><TD>writes energies to xvg files and displays averages</TD>
<TR><TD><A HREF="online/g_enemat.html">g_enemat</A></TD><TD>extracts an energy matrix from an energy file</TD>
+<TR><TD><A HREF="online/g_energy.html">g_energy</A></TD><TD>writes energies to xvg files and displays averages</TD>
<TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>with -rerun (re)calculates energies for trajectory frames</TD>
</TABLE>
<TR><TD>
<TR><TD COLSPAN=2><b>Converting files</b>
<TR><TD><A HREF="online/editconf.html">editconf</A></TD><TD>converts and manipulates structure files</TD>
-<TR><TD><A HREF="online/trjconv.html">trjconv</A></TD><TD>converts and manipulates trajectory files</TD>
-<TR><TD><A HREF="online/trjcat.html">trjcat</A></TD><TD>concatenates trajectory files</TD>
<TR><TD><A HREF="online/eneconv.html">eneconv</A></TD><TD>converts energy files</TD>
-<TR><TD><A HREF="online/xpm2ps.html">xpm2ps</A></TD><TD>converts XPM matrices to encapsulated postscript (or XPM)</TD>
<TR><TD><A HREF="online/g_sigeps.html">g_sigeps</A></TD><TD>convert c6/12 or c6/cn combinations to and from sigma/epsilon</TD>
+<TR><TD><A HREF="online/trjcat.html">trjcat</A></TD><TD>concatenates trajectory files</TD>
+<TR><TD><A HREF="online/trjconv.html">trjconv</A></TD><TD>converts and manipulates trajectory files</TD>
+<TR><TD><A HREF="online/xpm2ps.html">xpm2ps</A></TD><TD>converts XPM matrices to encapsulated postscript (or XPM)</TD>
</TABLE>
<A NAME="HNR6">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Tools</b>
-<TR><TD><A HREF="online/make_ndx.html">make_ndx</A></TD><TD>makes index files</TD>
-<TR><TD><A HREF="online/mk_angndx.html">mk_angndx</A></TD><TD>generates index files for g_angle</TD>
-<TR><TD><A HREF="online/gmxcheck.html">gmxcheck</A></TD><TD>checks and compares files</TD>
-<TR><TD><A HREF="online/gmxdump.html">gmxdump</A></TD><TD>makes binary files human readable</TD>
-<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v and f of selected atoms/groups (and more) from a trajectory</TD>
<TR><TD><A HREF="online/g_analyze.html">g_analyze</A></TD><TD>analyzes data sets</TD>
-<TR><TD><A HREF="online/trjorder.html">trjorder</A></TD><TD>orders molecules according to their distance to a group</TD>
+<TR><TD><A HREF="online/g_dyndom.html">g_dyndom</A></TD><TD>interpolate and extrapolate structure rotations</TD>
<TR><TD><A HREF="online/g_filter.html">g_filter</A></TD><TD>frequency filters trajectories, useful for making smooth movies</TD>
<TR><TD><A HREF="online/g_lie.html">g_lie</A></TD><TD>free energy estimate from linear combinations</TD>
-<TR><TD><A HREF="online/g_dyndom.html">g_dyndom</A></TD><TD>interpolate and extrapolate structure rotations</TD>
<TR><TD><A HREF="online/g_morph.html">g_morph</A></TD><TD>linear interpolation of conformations </TD>
-<TR><TD><A HREF="online/g_wham.html">g_wham</A></TD><TD>weighted histogram analysis after umbrella sampling</TD>
-<TR><TD><A HREF="online/xpm2ps.html">xpm2ps</A></TD><TD>convert XPM (XPixelMap) file to postscript</TD>
+<TR><TD><A HREF="online/g_pme_error.html">g_pme_error</A></TD><TD>estimates the error of using PME with a given input file</TD>
+<TR><TD><A HREF="online/g_select.html">g_select</A></TD><TD>selects groups of atoms based on flexible textual selections</TD>
<TR><TD><A HREF="online/g_sham.html">g_sham</A></TD><TD>read/write xmgr and xvgr data sets</TD>
<TR><TD><A HREF="online/g_spatial.html">g_spatial</A></TD><TD>calculates the spatial distribution function</TD>
-<TR><TD><A HREF="online/g_select.html">g_select</A></TD><TD>selects groups of atoms based on flexible textual selections</TD>
+<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v and f of selected atoms/groups (and more) from a trajectory</TD>
<TR><TD><A HREF="online/g_tune_pme.html">g_tune_pme</A></TD><TD>time mdrun as a function of PME nodes to optimize settings</TD>
+<TR><TD><A HREF="online/g_wham.html">g_wham</A></TD><TD>weighted histogram analysis after umbrella sampling</TD>
+<TR><TD><A HREF="online/gmxcheck.html">gmxcheck</A></TD><TD>checks and compares files</TD>
+<TR><TD><A HREF="online/gmxdump.html">gmxdump</A></TD><TD>makes binary files human readable</TD>
+<TR><TD><A HREF="online/make_ndx.html">make_ndx</A></TD><TD>makes index files</TD>
+<TR><TD><A HREF="online/mk_angndx.html">mk_angndx</A></TD><TD>generates index files for g_angle</TD>
+<TR><TD><A HREF="online/trjorder.html">trjorder</A></TD><TD>orders molecules according to their distance to a group</TD>
+<TR><TD><A HREF="online/xpm2ps.html">xpm2ps</A></TD><TD>convert XPM (XPixelMap) file to postscript</TD>
</TABLE>
<A NAME="HNR7">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Distances between structures</b>
-<TR><TD><A HREF="online/g_rms.html">g_rms</A></TD><TD>calculates rmsd's with a reference structure and rmsd matrices</TD>
-<TR><TD><A HREF="online/g_confrms.html">g_confrms</A></TD><TD>fits two structures and calculates the rmsd </TD>
<TR><TD><A HREF="online/g_cluster.html">g_cluster</A></TD><TD>clusters structures</TD>
+<TR><TD><A HREF="online/g_confrms.html">g_confrms</A></TD><TD>fits two structures and calculates the rmsd </TD>
+<TR><TD><A HREF="online/g_rms.html">g_rms</A></TD><TD>calculates rmsd's with a reference structure and rmsd matrices</TD>
<TR><TD><A HREF="online/g_rmsf.html">g_rmsf</A></TD><TD>calculates atomic fluctuations</TD>
</TABLE>
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Distances in structures over time</b>
-<TR><TD><A HREF="online/g_mindist.html">g_mindist</A></TD><TD>calculates the minimum distance between two groups</TD>
-<TR><TD><A HREF="online/g_dist.html">g_dist</A></TD><TD>calculates the distances between the centers of mass of two groups</TD>
<TR><TD><A HREF="online/g_bond.html">g_bond</A></TD><TD>calculates distances between atoms</TD>
+<TR><TD><A HREF="online/g_dist.html">g_dist</A></TD><TD>calculates the distances between the centers of mass of two groups</TD>
+<TR><TD><A HREF="online/g_mindist.html">g_mindist</A></TD><TD>calculates the minimum distance between two groups</TD>
<TR><TD><A HREF="online/g_mdmat.html">g_mdmat</A></TD><TD>calculates residue contact maps</TD>
<TR><TD><A HREF="online/g_polystat.html">g_polystat</A></TD><TD>calculates static properties of polymers</TD>
<TR><TD><A HREF="online/g_rmsdist.html">g_rmsdist</A></TD><TD>calculates atom pair distances averaged with power -2, -3 or -6</TD>
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Mass distribution properties over time</b>
-<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v, f, box, temperature and rotational energy</TD>
<TR><TD><A HREF="online/g_gyrate.html">g_gyrate</A></TD><TD>calculates the radius of gyration</TD>
<TR><TD><A HREF="online/g_msd.html">g_msd</A></TD><TD>calculates mean square displacements</TD>
<TR><TD><A HREF="online/g_polystat.html">g_polystat</A></TD><TD>calculates static properties of polymers</TD>
-<TR><TD><A HREF="online/g_rotacf.html">g_rotacf</A></TD><TD>calculates the rotational correlation function for molecules</TD>
<TR><TD><A HREF="online/g_rdf.html">g_rdf</A></TD><TD>calculates radial distribution functions</TD>
+<TR><TD><A HREF="online/g_rotacf.html">g_rotacf</A></TD><TD>calculates the rotational correlation function for molecules</TD>
<TR><TD><A HREF="online/g_rotmat.html">g_rotmat</A></TD><TD>plots the rotation matrix for fitting to a reference structure</TD>
+<TR><TD><A HREF="online/g_sans.html">g_sans</A></TD><TD>computes the small angle neutron scattering spectra</TD>
+<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v, f, box, temperature and rotational energy</TD>
<TR><TD><A HREF="online/g_vanhove.html">g_vanhove</A></TD><TD>calculates Van Hove displacement functions</TD>
</TABLE>
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Analyzing bonded interactions</b>
+<TR><TD><A HREF="online/g_angle.html">g_angle</A></TD><TD>calculates distributions and correlations for angles and dihedrals</TD>
<TR><TD><A HREF="online/g_bond.html">g_bond</A></TD><TD>calculates bond length distributions</TD>
<TR><TD><A HREF="online/mk_angndx.html">mk_angndx</A></TD><TD>generates index files for g_angle</TD>
-<TR><TD><A HREF="online/g_angle.html">g_angle</A></TD><TD>calculates distributions and correlations for angles and dihedrals</TD>
</TABLE>
<A NAME="HNR11">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Structural properties</b>
+<TR><TD><A HREF="online/g_anadock.html">g_anadock</A></TD><TD>cluster structures from Autodock runs</TD>
+<TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. helices</TD>
+<TR><TD><A HREF="online/g_clustsize.html">g_clustsize</A></TD><TD>calculate size distributions of atomic clusters</TD>
+<TR><TD><A HREF="online/g_disre.html">g_disre</A></TD><TD>analyzes distance restraints</TD>
<TR><TD><A HREF="online/g_hbond.html">g_hbond</A></TD><TD>computes and analyzes hydrogen bonds</TD>
-<TR><TD><A HREF="online/g_saltbr.html">g_saltbr</A></TD><TD>computes salt bridges</TD>
-<TR><TD><A HREF="online/g_sas.html">g_sas</A></TD><TD>computes solvent accessible surface area</TD>
<TR><TD><A HREF="online/g_order.html">g_order</A></TD><TD>computes the order parameter per atom for carbon tails</TD>
<TR><TD><A HREF="online/g_principal.html">g_principal</A></TD><TD>calculates axes of inertia for a group of atoms</TD>
<TR><TD><A HREF="online/g_rdf.html">g_rdf</A></TD><TD>calculates radial distribution functions</TD>
+<TR><TD><A HREF="online/g_saltbr.html">g_saltbr</A></TD><TD>computes salt bridges</TD>
+<TR><TD><A HREF="online/g_sas.html">g_sas</A></TD><TD>computes solvent accessible surface area</TD>
<TR><TD><A HREF="online/g_sgangle.html">g_sgangle</A></TD><TD>computes the angle and distance between two groups</TD>
<TR><TD><A HREF="online/g_sorient.html">g_sorient</A></TD><TD>analyzes solvent orientation around solutes</TD>
<TR><TD><A HREF="online/g_spol.html">g_spol</A></TD><TD>analyzes solvent dipole orientation and polarization around solutes</TD>
-<TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. helices</TD>
-<TR><TD><A HREF="online/g_disre.html">g_disre</A></TD><TD>analyzes distance restraints</TD>
-<TR><TD><A HREF="online/g_clustsize.html">g_clustsize</A></TD><TD>calculate size distributions of atomic clusters</TD>
-<TR><TD><A HREF="online/g_anadock.html">g_anadock</A></TD><TD>cluster structures from Autodock runs</TD>
</TABLE>
<A NAME="HNR12">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Kinetic properties</b>
-<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v, f, box, temperature and rotational energy</TD>
-<TR><TD><A HREF="online/g_velacc.html">g_velacc</A></TD><TD>calculates velocity autocorrelation functions</TD>
-<TR><TD><A HREF="online/g_tcaf.html">g_tcaf</A></TD><TD>calculates viscosities of liquids</TD>
<TR><TD><A HREF="online/g_bar.html">g_bar</A></TD><TD>calculates free energy difference estimates through Bennett's acceptance ratio</TD>
<TR><TD><A HREF="online/g_current.html">g_current</A></TD><TD>calculate current autocorrelation function of system</TD>
-<TR><TD><A HREF="online/g_vanhove.html">g_vanhove</A></TD><TD>compute Van Hove correlation function</TD>
+<TR><TD><A HREF="online/g_dos.html">g_dos</A></TD><TD>analyzes density of states and properties based on that</TD>
+<TR><TD><A HREF="online/g_dyecoupl.html">g_dyecoupl</A></TD><TD>extracts dye dynamics from trajectories</TD>
+<TR><TD><A HREF="online/g_kinetics.html">g_kinetics</A></TD><TD>analyzes kinetic constants from properties based on the Eyring model</TD>
<TR><TD><A HREF="online/g_principal.html">g_principal</A></TD><TD>calculate principal axes of inertion for a group of atoms</TD>
+<TR><TD><A HREF="online/g_tcaf.html">g_tcaf</A></TD><TD>calculates viscosities of liquids</TD>
+<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v, f, box, temperature and rotational energy</TD>
+<TR><TD><A HREF="online/g_vanhove.html">g_vanhove</A></TD><TD>compute Van Hove correlation function</TD>
+<TR><TD><A HREF="online/g_velacc.html">g_velacc</A></TD><TD>calculates velocity autocorrelation functions</TD>
</TABLE>
<A NAME="HNR13">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Electrostatic properties</b>
-<TR><TD><A HREF="online/genion.html">genion</A></TD><TD>generates mono atomic ions on energetically favorable positions</TD>
-<TR><TD><A HREF="online/g_potential.html">g_potential</A></TD><TD>calculates the electrostatic potential across the box</TD>
-<TR><TD><A HREF="online/g_dipoles.html">g_dipoles</A></TD><TD>computes the total dipole plus fluctuations</TD>
-<TR><TD><A HREF="online/g_dielectric.html">g_dielectric</A></TD><TD>calculates frequency dependent dielectric constants</TD>
<TR><TD><A HREF="online/g_current.html">g_current</A></TD><TD>calculates dielectric constants for charged systems</TD>
+<TR><TD><A HREF="online/g_dielectric.html">g_dielectric</A></TD><TD>calculates frequency dependent dielectric constants</TD>
+<TR><TD><A HREF="online/g_dipoles.html">g_dipoles</A></TD><TD>computes the total dipole plus fluctuations</TD>
+<TR><TD><A HREF="online/g_potential.html">g_potential</A></TD><TD>calculates the electrostatic potential across the box</TD>
<TR><TD><A HREF="online/g_spol.html">g_spol</A></TD><TD>analyze dipoles around a solute</TD>
+<TR><TD><A HREF="online/genion.html">genion</A></TD><TD>generates mono atomic ions on energetically favorable positions</TD>
</TABLE>
<A NAME="HNR14">
<TABLE CELLSPACING=1>
<TR><TD>
-<TR><TD COLSPAN=2><b>Protein specific analysis</b>
+<TR><TD COLSPAN=2><b>Protein-specific analysis</b>
<TR><TD><A HREF="online/do_dssp.html">do_dssp</A></TD><TD>assigns secondary structure and calculates solvent accessible surface area</TD>
<TR><TD><A HREF="online/g_chi.html">g_chi</A></TD><TD>calculates everything you want to know about chi and other dihedrals</TD>
<TR><TD><A HREF="online/g_helix.html">g_helix</A></TD><TD>calculates basic properties of alpha helices</TD>
<TR><TD><A HREF="online/g_helixorient.html">g_helixorient</A></TD><TD>calculates local pitch/bending/rotation/orientation inside helices</TD>
<TR><TD><A HREF="online/g_rama.html">g_rama</A></TD><TD>computes Ramachandran plots</TD>
-<TR><TD><A HREF="online/g_xrama.html">g_xrama</A></TD><TD>shows animated Ramachandran plots</TD>
<TR><TD><A HREF="online/g_wheel.html">g_wheel</A></TD><TD>plots helical wheels</TD>
+<TR><TD><A HREF="online/g_xrama.html">g_xrama</A></TD><TD>shows animated Ramachandran plots</TD>
</TABLE>
<A NAME="HNR15">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Interfaces</b>
-<TR><TD><A HREF="online/g_potential.html">g_potential</A></TD><TD>calculates the electrostatic potential across the box</TD>
+<TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. transmembrane helices</TD>
<TR><TD><A HREF="online/g_density.html">g_density</A></TD><TD>calculates the density of the system</TD>
<TR><TD><A HREF="online/g_densmap.html">g_densmap</A></TD><TD>calculates 2D planar or axial-radial density maps</TD>
-<TR><TD><A HREF="online/g_order.html">g_order</A></TD><TD>computes the order parameter per atom for carbon tails</TD>
+<TR><TD><A HREF="online/g_densorder.html">g_densorder</A></TD><TD>calculate surface fluctuations</TD>
<TR><TD><A HREF="online/g_h2order.html">g_h2order</A></TD><TD>computes the orientation of water molecules</TD>
-<TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. transmembrane helices</TD>
+<TR><TD><A HREF="online/g_hydorder.html">g_hydorder</A></TD><TD>computes tetrahedrality parameters around a given atom</TD>
+<TR><TD><A HREF="online/g_order.html">g_order</A></TD><TD>computes the order parameter per atom for carbon tails</TD>
<TR><TD><A HREF="online/g_membed.html">g_membed</A></TD><TD>embeds a protein into a lipid bilayer</TD>
+<TR><TD><A HREF="online/g_potential.html">g_potential</A></TD><TD>calculates the electrostatic potential across the box</TD>
</TABLE>
<A NAME="HNR16">
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Covariance analysis</b>
-<TR><TD><A HREF="online/g_covar.html">g_covar</A></TD><TD>calculates and diagonalizes the covariance matrix</TD>
<TR><TD><A HREF="online/g_anaeig.html">g_anaeig</A></TD><TD>analyzes the eigenvectors</TD>
+<TR><TD><A HREF="online/g_covar.html">g_covar</A></TD><TD>calculates and diagonalizes the covariance matrix</TD>
<TR><TD><A HREF="online/make_edi.html">make_edi</A></TD><TD>generate input files for essential dynamics sampling</TD>
</TABLE>
<TABLE CELLSPACING=1>
<TR><TD>
<TR><TD COLSPAN=2><b>Normal modes</b>
-<TR><TD><A HREF="online/grompp.html">grompp</A></TD><TD>makes a run input file</TD>
-<TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>finds a potential energy minimum</TD>
-<TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>calculates the Hessian</TD>
+<TR><TD><A HREF="online/g_anaeig.html">g_anaeig</A></TD><TD>analyzes the normal modes</TD>
<TR><TD><A HREF="online/g_nmeig.html">g_nmeig</A></TD><TD>diagonalizes the Hessian </TD>
<TR><TD><A HREF="online/g_nmtraj.html">g_nmtraj</A></TD><TD>generate oscillating trajectory of an eigenmode</TD>
-<TR><TD><A HREF="online/g_anaeig.html">g_anaeig</A></TD><TD>analyzes the normal modes</TD>
<TR><TD><A HREF="online/g_nmens.html">g_nmens</A></TD><TD>generates an ensemble of structures from the normal modes</TD>
+<TR><TD><A HREF="online/grompp.html">grompp</A></TD><TD>makes a run input file</TD>
+<TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>finds a potential energy minimum and calculates the Hessian</TD>
</TABLE>
<p>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The cpt file extension stands for portable checkpoint file.
The complete state of the simulation is stored in the checkpoint file,
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Files with the dat file extension contain generic input or output.
As it is not possible
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The dlg file format is used as input for the <a href="ngmx.html">ngmx</a>
trajectory viewer. These files are not meant to be altered bu the end user.
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>do_dssp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-do_dssp
+<tt>do_dssp</tt>
reads a trajectory file and computes the secondary structure for
each time frame
calling the dssp program. If you do not have the dssp program,
-get it. do_dssp assumes that the dssp executable is
-/usr/local/bin/dssp. If this is not the case, then you should
-set an environment variable <b>DSSP</b> pointing to the dssp
+get it from http://swift.cmbi.ru.nl/gv/dssp. <tt>do_dssp</tt> assumes
+that the dssp executable is located in
+<tt>/usr/local/bin/dssp</tt>. If this is not the case, then you should
+set an environment variable <tt>DSSP</tt> pointing to the dssp
executable, e.g.: <p>
<tt>setenv DSSP /opt/dssp/bin/dssp</tt><p>
+Since version 2.0.0, dssp is invoked with a syntax that differs
+from earlier versions. If you have an older version of dssp,
+use the <tt>-ver</tt> option to direct do_dssp to use the older syntax.
+By default, do_dssp uses the syntax introduced with version 2.0.0.
+Even newer versions (which at the time of writing are not yet released)
+are assumed to have the same syntax as 2.0.0.<p>
The structure assignment for each residue and time is written to an
<tt>.<a href="xpm.html">xpm</a></tt> matrix file. This file can be visualized with for instance
<tt>xv</tt> and can be converted to postscript with <tt><a href="xpm2ps.html">xpm2ps</a></tt>.
-Individual chains are separated by light grey lines in the <a href="xpm.html">xpm</a> and
+Individual chains are separated by light grey lines in the <tt>.<a href="xpm.html">xpm</a></tt> and
postscript files.
The number of residues with each secondary structure type and the
total secondary structure (<tt>-sss</tt>) count as a function of
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-sss</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>HEBT</tt> </TD><TD> Secondary structures for structure count </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ver</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> DSSP major version. Syntax changed with version 2 </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Files with the edi file extension contain information for <a href="mdrun.html">
mdrun</a> to run Molecular Dynamics with Essential Dynamics constraints.
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>editconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-
editconf converts generic structure format to <tt>.<a href="gro.html">gro</a></tt>, <tt>.<a href="g96.html">g96</a></tt>
+
<tt>editconf</tt> converts generic structure format to <tt>.<a href="gro.html">gro</a></tt>, <tt>.<a href="g96.html">g96</a></tt>
or <tt>.<a href="pdb.html">pdb</a></tt>.
<p>
The box can be modified with options <tt>-box</tt>, <tt>-d</tt> and
The last two are special cases of a triclinic box.
The length of the three box vectors of the truncated octahedron is the
shortest distance between two opposite hexagons.
-The volume of a dodecahedron is 0.71 and that of a truncated octahedron
-is 0.77 of that of a cubic box with the same periodic image distance.
+Relative to a cubic box with some periodic image distance, the volume of a
+dodecahedron with this same periodic distance is 0.71 times that of the cube,
+and that of a truncated octahedron is 0.77 times.
<p>
Option <tt>-box</tt> requires only
-one value for a cubic box, dodecahedron and a truncated octahedron.
+one value for a cubic, rhombic dodecahedral, or truncated octahedral box.
<p>
-With <tt>-d</tt> and a <tt>triclinic</tt> box the size of the system in the x, y
-and z directions is used. With <tt>-d</tt> and <tt>cubic</tt>,
+With <tt>-d</tt> and a <tt>triclinic</tt> box the size of the system in the <it>x</it>-, <it>y</it>-,
+and <it>z</it>-directions is used. With <tt>-d</tt> and <tt>cubic</tt>,
<tt>dodecahedron</tt> or <tt>octahedron</tt> boxes, the dimensions are set
to the diameter of the system (largest distance between atoms) plus twice
the specified distance.
<p>
Option <tt>-angles</tt> is only meaningful with option <tt>-box</tt> and
-a triclinic box and can not be used with option <tt>-d</tt>.
+a triclinic box and cannot be used with option <tt>-d</tt>.
<p>
When <tt>-n</tt> or <tt>-ndef</tt> is set, a group
can be selected for calculating the size and the geometric center,
<tt>-rotate</tt> rotates the coordinates and velocities.
<p>
<tt>-princ</tt> aligns the principal axes of the system along the
-coordinate axes, this may allow you to decrease the box volume,
+coordinate axes, with the longest axis aligned with the <it>x</it>-axis.
+This may allow you to decrease the box volume,
but beware that molecules can rotate significantly in a nanosecond.
<p>
Scaling is applied before any of the other operations are
performed. Boxes and coordinates can be scaled to give a certain density (option
-<tt>-density</tt>). Note that this may be inaccurate in case a <a href="gro.html">gro</a>
-file is given as input. A special feature of the scaling option, when the
+<tt>-density</tt>). Note that this may be inaccurate in case a <tt>.<a href="gro.html">gro</a></tt>
+file is given as input. A special feature of the scaling option is that when the
factor -1 is given in one dimension, one obtains a mirror image,
-mirrored in one of the plains, when one uses -1 in three dimensions
+mirrored in one of the planes. When one uses -1 in three dimensions,
a point-mirror image is obtained.<p>
Groups are selected after all operations have been applied.<p>
Periodicity can be removed in a crude manner.
-It is important that the box sizes at the bottom of your input file
+It is important that the box vectors at the bottom of your input file
are correct when the periodicity is to be removed.
<p>
When writing <tt>.<a href="pdb.html">pdb</a></tt> files, B-factors can be
a row of CA atoms with B-factors ranging from the minimum to the
maximum value found, effectively making a legend for viewing.
<p>
-With the option -mead a special <a href="pdb.html">pdb</a> (pqr) file for the MEAD electrostatics
+With the option <tt>-mead</tt> a special <tt>.<a href="pdb.html">pdb</a></tt> (<tt>.pqr</tt>)
+file for the MEAD electrostatics
program (Poisson-Boltzmann solver) can be made. A further prerequisite
is that the input file is a run input file.
The B-factor field is then filled with the Van der Waals radius
of the atoms while the occupancy field will hold the charge.
<p>
-The option -grasp is similar, but it puts the charges in the B-factor
+The option <tt>-grasp</tt> is similar, but it puts the charges in the B-factor
and the radius in the occupancy.
<p>
Option <tt>-align</tt> allows alignment
of the principal axis of a specified group against the given vector,
with an optional center of rotation specified by <tt>-aligncenter</tt>.
<p>
-Finally with option <tt>-label</tt> editconf can add a chain identifier
-to a <a href="pdb.html">pdb</a> file, which can be useful for analysis with e.g. rasmol.
+Finally, with option <tt>-label</tt>, <tt>editconf</tt> can add a chain identifier
+to a <tt>.<a href="pdb.html">pdb</a></tt> file, which can be useful for analysis with e.g. Rasmol.
<p>
To convert a truncated octrahedron file produced by a package which uses
-a cubic box with the corners cut off (such as Gromos) use:<br>
-<tt>editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out></tt><br>
+a cubic box with the corners cut off (such as GROMOS), use:<br>
+<tt>editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out</tt><br>
where <tt>veclen</tt> is the size of the cubic box times sqrt(3)/2.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ndef</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Choose output from default index groups </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bt</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>triclinic</tt> </TD><TD> Box type for -box and -d: <tt>triclinic</tt>, <tt>cubic</tt>, <tt>dodecahedron</tt> or <tt>octahedron</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ndef</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Choose output from default index groups </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bt</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>triclinic</tt> </TD><TD> Box type for <tt>-box</tt> and <tt>-d</tt>: <tt>triclinic</tt>, <tt>cubic</tt>, <tt>dodecahedron</tt> or <tt>octahedron</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Box vector lengths (a,b,c) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-angles</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>90 90 90</tt> </TD><TD> Angles between the box vectors (bc,ac,ab) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Distance between the solute and the box </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]c</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Center molecule in box (implied by -box and -d) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]c</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Center molecule in box (implied by <tt>-box</tt> and <tt>-d</tt>) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-center</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Coordinates of geometrical center </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-aligncenter</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Center of rotation for alignment </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-align</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Align to target vector </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-translate</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Translation </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rotate</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Rotation around the X, Y and Z axes in degrees </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]princ</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Orient molecule(s) along their principal axes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]princ</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Orient molecule(s) along their principal axes </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Scaling factor </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-density</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000 </tt> </TD><TD> Density (g/l) of the output box achieved by scaling </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove the periodicity (make molecule whole again) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]grasp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-density</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000 </tt> </TD><TD> Density (g/L) of the output box achieved by scaling </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove the periodicity (make molecule whole again) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-resnr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Renumber residues starting from resnr </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]grasp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rvdw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.12 </tt> </TD><TD> Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sig56</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vdwread</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Read the Van der Waals radii from the file vdwradii.<a href="dat.html">dat</a> rather than computing the radii based on the force field </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]atom</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Force B-factor attachment per atom </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]legend</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Make B-factor legend </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sig56</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use rmin/2 (minimum in the Van der Waals potential) rather than σ/2 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vdwread</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Read the Van der Waals radii from the file <tt>vdwradii.<a href="dat.html">dat</a></tt> rather than computing the radii based on the force field </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]atom</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Force B-factor attachment per atom </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]legend</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Make B-factor legend </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-label</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>A</tt> </TD><TD> Add chain label for all residues </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]conect</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Add CONECT records to a <a href="pdb.html">pdb</a> file when written. Can only be done when a topology is present </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]conect</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Add CONECT records to a <tt>.<a href="pdb.html">pdb</a></tt> file when written. Can only be done when a topology is present </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<UL>
-<LI>For complex molecules, the periodicity removal routine may break down,
-<LI>in that case you can use <a href="trjconv.html">trjconv</a>.
+<LI>For complex molecules, the periodicity removal routine may break down, in that case you can use <tt><a href="trjconv.html">trjconv</a></tt>.
</UL>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Files with the edo file extension are generated by <a href="mdrun.html">
mdrun</a> if Molecular Dynamics is performed with Essential Dynamics
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The edr file extension stands for portable energy file.
The energies are stored using the xdr protocol.
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The ene file extension stands for binary energy file. It holds the
energies as generated during your <a href="mdrun.html">mdrun</a>.
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>eneconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
With <it>multiple files</it> specified for the <tt>-f</tt> option:<br>
Concatenates several energy files in sorted order.
-In case of double time frames the one
+In the case of double time frames, the one
in the later file is used. By specifying <tt>-settime</tt> you will be
asked for the start time of each file. The input files are taken
from the command line,
-such that the command <tt>eneconv -
o fixed.<a href="edr.html">edr</a> *.<a href="edr.html">edr</a></tt> should do
+such that the command <tt>eneconv -
f *.<a href="edr.html">edr</a> -o fixed.<a href="edr.html">edr</a></tt> should do
the trick. <p>
With <it>one file</it> specified for <tt>-f</tt>:<br>
Reads one energy file and writes another, applying the <tt>-dt</tt>,
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> First time to use </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Last time to use </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only write out frame when t MOD dt = offset </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-offset</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time offset for -dt option </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change starting time interactively </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Sort energy files (not frames) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-offset</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time offset for <tt>-dt</tt> option </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change starting time interactively </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Sort energy files (not frames) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmdh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove free energy block data </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-scalefac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Multiply energy component by this factor </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]error</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Stop on errors in the file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]error</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Stop on errors in the file </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The eps file format is not a special GROMACS format, but just a
variant of the standard PostScript(tm). A sample eps file as
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>File Formats</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<dl>
<dt><h3>Parameter files</h3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>Flow chart</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<p>This is a flow chart of a typical GROMACS MD run of a protein
in a box of water.
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
This is a simple ASCII format:<br>
<pre>
TITLE
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<p>A file with the g96 extension can be a GROMOS-96 initial/final
configuration file or a coordinate trajectory file or a combination of both.
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_anadock</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-anadock analyses the results of an Autodock run and clusters the
+<tt>g_anadock</tt> analyses the results of an Autodock run and clusters the
structures together, based on distance or RMSD. The docked energy
and free energy estimates are analysed, and for each cluster the
energy statistics are printed.<p>
An alternative approach to this is to cluster the structures first
-
(using <tt><a href="g_cluster.html">g_cluster</a></tt> and then sort the clusters on either lowest
+using <tt><a href="g_cluster.html">g_cluster</a></tt> and then sort the clusters on either lowest
energy or average energy.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]free</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use Free energy estimate from autodock for sorting the classes </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rms</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Cluster on RMS or distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]free</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use Free energy estimate from autodock for sorting the classes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rms</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Cluster on RMS or distance </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.2 </tt> </TD><TD> Maximum RMSD/distance for belonging to the same cluster </TD></TD>
</TABLE>
<P>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_anaeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<tt>-last</tt> have been set explicitly, in which case all eigenvectors
will be written to separate files. Chain identifiers will be added
when writing a <tt>.<a href="pdb.html">pdb</a></tt> file with two or three structures (you
-can use <tt>rasmol -nmrpdb</tt> to view such a <
a href="pdb.html">pdb</a> file).<p>
+can use <tt>rasmol -nmrpdb</tt> to view such a <
tt>.<a href="pdb.html">pdb</a></tt> file).<p>
Overlap calculations between covariance analysis:<br>
-
NOTE: the analysis should use the same fitting structure<p>
+
<b>Note:</b> the analysis should use the same fitting structure<p>
<tt>-over</tt>: calculate the subspace overlap of the eigenvectors in
file <tt>-v2</tt> with eigenvectors <tt>-first</tt> to <tt>-last</tt>
in file <tt>-v</tt>.<p>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> First eigenvector for analysis (-1 is select) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>8</tt> </TD><TD> Last eigenvector for analysis (-1 is till the last) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Last eigenvector for analysis (-1 is till the last) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyse every nr-th frame </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nframes</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> Number of frames for the extremes output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split eigenvector projections where time is zero </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]entropy</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute entropy according to the Quasiharmonic formula or Schlitter's method. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split eigenvector projections where time is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]entropy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute entropy according to the Quasiharmonic formula or Schlitter's method. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for entropy calculations </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nevskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>6</tt> </TD><TD> Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and which should not be taken into account when computing the entropy. </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_analyze</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_analyze reads an ascii file and analyzes data sets.
+<tt>g_analyze</tt> reads an ASCII file and analyzes data sets.
A line in the input file may start with a time
-(see option <tt>-time</tt>) and any number of y values may follow.
+(see option <tt>-time</tt>) and any number of <it>y</it>-values may follow.
Multiple sets can also be
-read when they are separated by & (option <tt>-n</tt>),
-in this case only one y value is read from each line.
+read when they are separated by & (option <tt>-n</tt>);
+in this case only one <it>y</it>-value is read from each line.
All lines starting with # and @ are skipped.
All analyses can also be done for the derivative of a set
(option <tt>-d</tt>).<p>
-All options, except for <tt>-av</tt> and <tt>-power</tt> assume that the
+All options, except for <tt>-av</tt> and <tt>-power</tt>, assume that the
points are equidistant in time.<p>
-g_analyze always shows the average and standard deviation of each
-set. For each set it also shows the relative deviation of the third
+<tt>g_analyze</tt> always shows the average and standard deviation of each
+set, as well as the relative deviation of the third
and fourth cumulant from those of a Gaussian distribution with the same
standard deviation.<p>
-Option <tt>-ac</tt> produces the autocorrelation function(s).<p>
+Option <tt>-ac</tt> produces the autocorrelation function(s).
+Be sure that the time interval between data points is
+much shorter than the time scale of the autocorrelation.<p>
Option <tt>-cc</tt> plots the resemblance of set i with a cosine of
-i/2 periods. The formula is:<br>2 (int0-T y(t) cos(i pi t) dt)^2 / int0-T y(t) y(t) dt<br>
+i/2 periods. The formula is:<br>2 (integral from 0 to T of y(t) cos(i π t) dt)^2 / integral from 0 to T of y^2(t) dt<br>
This is useful for principal components obtained from covariance
analysis, since the principal components of random diffusion are
pure cosines.<p>
A set is divided in a number of blocks and averages are calculated for
each block. The error for the total average is calculated from
the variance between averages of the m blocks B_i as follows:
-error^2 = Sum (B_i - <B>)^2 / (m*(m-1)).
+error^2 = sum (B_i - <B>)^2 / (m*(m-1)).
These errors are plotted as a function of the block size.
Also an analytical block average curve is plotted, assuming
that the autocorrelation is a sum of two exponentials.
The analytical curve for the block average is:<br>
-f(t) = sigma sqrt(2/T ( a (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +<br>
- (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),<br>where T is the total time.
-a, tau1 and tau2 are obtained by fitting f^2(t) to error^2.
+f(t) = σ<tt>*</tt>sqrt(2/T ( α (τ_1 ((exp(-t/τ_1) - 1) τ_1/t + 1)) +<br>
+ (1-α) (τ_2 ((exp(-t/τ_2) - 1) τ_2/t + 1)))),<br>where T is the total time.
+α, τ_1 and τ_2 are obtained by fitting f^2(t) to error^2.
When the actual block average is very close to the analytical curve,
-the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).
+the error is σ<tt>*</tt>sqrt(2/T (a τ_1 + (1-a) τ_2)).
The complete derivation is given in
B. Hess, J. Chem. Phys. 116:209-217, 2002.<p>
Option <tt>-bal</tt> finds and subtracts the ultrafast "ballistic"
Option <tt>-gem</tt> fits bimolecular rate constants ka and kb
(and optionally kD) to the hydrogen bond autocorrelation function
according to the reversible geminate recombination model. Removal of
-the ballistic component first is strongly adviced. The model is presented in
+the ballistic component first is strongly advised. The model is presented in
O. Markovitch, J. Chem. Phys. 129:084505, 2008.<p>
Option <tt>-filter</tt> prints the RMS high-frequency fluctuation
of each set and over all sets with respect to a filtered average.
-The filter is proportional to cos(pi t/len) where t goes from -len/2
+The filter is proportional to cos(π t/len) where t goes from -len/2
to len/2. len is supplied with the option <tt>-filter</tt>.
This filter reduces oscillations with period len/2 and len by a factor
of 0.79 and 0.33 respectively.<p>
<tt>-fitfn</tt>.<p>
Option <tt>-power</tt> fits the data to b t^a, which is accomplished
by fitting to a t + b on <a href="log.html">log</a>-<a href="log.html">log</a> scale. All points after the first
-zero or negative value are ignored.<p>Option <tt>-luzar</tt> performs a Luzar & Chandler kinetics analysis
+zero or
with a negative value are ignored.<p>Option <tt>-luzar</tt> performs a Luzar & Chandler kinetics analysis
on output from <tt><a href="g_hbond.html">g_hbond</a></tt>. The input file can be taken directly
from <tt><a href="g_hbond.html">g_hbond</a> -ac</tt>, and then the same result should be produced.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Expect a time in the input </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Expect a time in the input </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> First time to read from set </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Last time to read from set </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read # sets separated by & </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the derivative </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read this number of sets separated by & </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the derivative </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Binwidth for the distribution </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-errbar</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Error bars for -av: <tt>none</tt>, <tt>stddev</tt>, <tt>error</tt> or <tt>90</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]integrate</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Integrate data function(s) numerically using trapezium rule </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-errbar</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Error bars for <tt>-av</tt>: <tt>none</tt>, <tt>stddev</tt>, <tt>error</tt> or <tt>90</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]integrate</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Integrate data function(s) numerically using trapezium rule </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-aver_start</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Start averaging the integral from here </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xydy</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interpret second data set as error in the y values for integrating </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]regression</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Perform a linear regression analysis on the data. If -xydy is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi^2 = (y - A0 x0 - A1 x1 - ... - AN xN)^2 where now Y is the first data set in the input file and xi the others. Do read the information at the option <tt>-time</tt>. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]luzar</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a Luzar and Chandler analysis on a correlation function and related as produced by <a href="g_hbond.html">g_hbond</a>. When in addition the -xydy flag is given the second and fourth column will be interpreted as errors in c(t) and n(t). </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for the Luzar hydrogen bonding kinetics analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xydy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interpret second data set as error in the y values for integrating </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]regression</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Perform a linear regression analysis on the data. If <tt>-xydy</tt> is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize χ^2 = (y - A_0 x_0 - A_1 x_1 - ... - A_N x_N)^2 where now Y is the first data set in the input file and x_i the others. Do read the information at the option <tt>-time</tt>. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]luzar</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a Luzar and Chandler analysis on a correlation function and related as produced by <tt><a href="g_hbond.html">g_hbond</a></tt>. When in addition the <tt>-xydy</tt> flag is given the second and fourth column will be interpreted as errors in c(t) and n(t). </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for the Luzar hydrogen bonding kinetics analysis (K) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>60 </tt> </TD><TD> Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with -gem </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-smooth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-filter</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Print the high-frequency fluctuation after filtering with a cosine filter of length # </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]power</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Fit data to: b t^a </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]subav</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Subtract the average before autocorrelating </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]oneacf</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate one ACF over all sets </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>60 </tt> </TD><TD> Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with <tt>-gem</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-smooth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> If this value is >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/τ) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-filter</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Print the high-frequency fluctuation after filtering with a cosine filter of this length </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]power</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Fit data to: b t^a </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]subav</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Subtract the average before autocorrelating </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]oneacf</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate one ACF over all sets </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_angle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_angle computes the angle distribution for a number of angles
-or dihedrals. This way you can check whether your simulation
-is correct. With option -ov you can plot the average angle of
-a group of angles as a function of time. With the -all option
-the first graph is the average
, the rest are the individual angles.<p>
-With the -of option g_angle also calculates the fraction of trans
+<tt>g_angle</tt> computes the angle distribution for a number of angles
+or dihedrals.<p>
+With option <tt>-ov</tt>, you can plot the average angle of
+a group of angles as a function of time. With the <tt>-all</tt> option,
+the first graph is the average
and the rest are the individual angles.<p>
+With the <tt>-of</tt> option, <tt>g_angle</tt> also calculates the fraction of trans
dihedrals (only for dihedrals) as function of time, but this is
-probably only fun for a select
ed few.<p>
-With option
-oc a dihedral correlation function is calculated.<p>
-It should be noted that the indexfile should contain
-atom-triples for angles or atom-quadruplets for dihedrals.
+probably only fun for a select few.<p>
+With option
<tt>-oc</tt>, a dihedral correlation function is calculated.<p>
+It should be noted that the index file must contain
+atom triplets for angles or atom quadruplets for dihedrals.
If this is not the case, the program will crash.<p>
-With option <tt>-or</tt> a trajectory file is dumped containing cos and
-sin of selected dihedral angles which subsequently can be used as
-input for a PCA analysis using <tt><a href="g_covar.html">g_covar</a></tt>.
+With option <tt>-or</tt>, a trajectory file is dumped containing cos and
+sin of selected dihedral angles, which subsequently can be used as
+input for a principal components analysis using <tt><a href="g_covar.html">g_covar</a></tt>.<p>
+Option <tt>-ot</tt> plots when transitions occur between
+dihedral rotamers of multiplicity 3 and <tt>-oh</tt>
+records a histogram of the times between such transitions,
+assuming the input trajectory frames are equally spaced in time.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle to analyse: <tt>angle</tt>, <tt>dihedral</tt>, <tt>improper</tt> or <tt>ryckaert-bellemans</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot all angles separately in the averages file, in the order of appearance in the index file. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot all angles separately in the averages file, in the order of appearance in the index file. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-binwidth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> binwidth (degrees) for calculating the distribution </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]periodic</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print dihedral angles modulo 360 degrees </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]chandler</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 || phi > 60. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]avercorr</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Average the correlation functions for the individual angles/dihedrals </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]periodic</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print dihedral angles modulo 360 degrees </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]chandler</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 or phi > 60. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]avercorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Average the correlation functions for the individual angles/dihedrals </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bar</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_bar calculates free energy difference estimates through
-Bennett's acceptance ratio method.
-Input option <tt>-f</tt> expects multiple dhdl files.
+<tt>g_bar</tt> calculates free energy difference estimates through
+Bennett's acceptance ratio method (BAR). It also automatically
+adds series of individual free energies obtained with BAR into
+a combined free energy estimate.<p>
+Every individual BAR free energy difference relies on two
+simulations at different states: say state A and state B, as
+controlled by a parameter, λ (see the <tt>.<a href="mdp.html">mdp</a></tt> parameter
+<tt>init_lambda</tt>). The BAR method calculates a ratio of weighted
+average of the Hamiltonian difference of state B given state A and
+vice versa.
+The energy differences to the other state must be calculated
+explicitly during the simulation. This can be done with
+the <tt>.<a href="mdp.html">mdp</a></tt> option <tt>foreign_lambda</tt>.<p>
+Input option <tt>-f</tt> expects multiple <tt>dhdl.<a href="xvg.html">xvg</a></tt> files.
Two types of input files are supported:<br>
-* Files with only one y-value, for such files it is assumed
-that the y-value is dH/dlambda and that the Hamiltonian depends
-linearly on lambda. The lambda value of the simulation is inferred
-from the subtitle if present, otherwise from a number in the
-subdirectory in the file name.
+<tt>*</tt> Files with more than one <it>y</it>-value.
+The files should have columns
+with dH/dλ and Δλ.
+The λ values are inferred
+from the legends: λ of the simulation from the legend of
+dH/dλ and the foreign λ values from the
+legends of Delta H
<br>
-* Files with more than one y-value. The files should have columns
-with dH/dlambda and Delta lambda. The lambda values are inferred
-from the legends:
-lambda of the simulation from the legend of dH/dlambda
-and the foreign lambda's from the legends of Delta H.<p>
-The lambda of the simulation is parsed from dhdl.<a href="xvg.html">xvg</a> file's legend
-containing the string 'dH', the foreign lambda's from the legend
-containing the capitalized letters 'D' and 'H'. The temperature
-is parsed from the legend line containing 'T ='.<p>
+<tt>*</tt> Files with only one <it>y</it>-value. Using the
+<tt>-extp</tt> option for these files, it is assumed
+that the <it>y</it>-value is dH/dλ and that the
+Hamiltonian depends linearly on λ.
+The λ value of the simulation is inferred from the
+subtitle (if present), otherwise from a number in the subdirectory
+in the file name.<p>
+The λ of the simulation is parsed from
+<tt>dhdl.<a href="xvg.html">xvg</a></tt> file's legend containing the string 'dH', the
+foreign λ values from the legend containing the
+capitalized letters 'D' and 'H'. The temperature is parsed from
+the legend line containing 'T ='.<p>
+The input option <tt>-g</tt> expects multiple <tt>.<a href="edr.html">edr</a></tt> files.
+These can contain either lists of energy differences (see the
+<tt>.<a href="mdp.html">mdp</a></tt> option <tt>separate_dhdl_file</tt>), or a series of
+histograms (see the <tt>.<a href="mdp.html">mdp</a></tt> options <tt>dh_hist_size</tt> and
+<tt>dh_hist_spacing</tt>).
+The temperature and λ
+values are automatically deduced from the <tt>ener.<a href="edr.html">edr</a></tt> file.<p>
+In addition to the <tt>.<a href="mdp.html">mdp</a></tt> option <tt>foreign_lambda</tt>,
+the energy difference can also be extrapolated from the
+dH/dλ values. This is done with the<tt>-extp</tt>
+option, which assumes that the system's Hamiltonian depends linearly
+on λ, which is not normally the case.<p>
The free energy estimates are determined using BAR with bisection,
-the precision of the output is set with <tt>-prec</tt>.
+with the precision of the output set with <tt>-prec</tt>.
An error estimate taking into account time correlations
is made by splitting the data into blocks and determining
the free energy differences over those blocks and assuming
the blocks are independent.
The final error estimate is determined from the average variance
-over 5 blocks. A range of blocks numbers for error estimation can
+over 5 blocks. A range of block numbers for error estimation can
be provided with the options <tt>-nbmin</tt> and <tt>-nbmax</tt>.<p>
+<tt>g_bar</tt> tries to aggregate samples with the same 'native' and
+'foreign' λ values, but always assumes independent
+samples. <b>Note</b> that when aggregating energy
+differences/derivatives with different sampling intervals, this is
+almost certainly not correct. Usually subsequent energies are
+correlated and different time intervals mean different degrees
+of correlation between samples.<p>
The results are split in two parts: the last part contains the final
results in kJ/mol, together with the error estimate for each part
and the total. The first part contains detailed free energy
difference estimates and phase space overlap measures in units of
kT (together with their computed error estimate). The printed
values are:<br>
-* lam_A: the lambda values for point A.<br>
-* lam_B: the lambda values for point B.<br>
-* DG: the free energy estimate.<br>
-* s_A: an estimate of the relative entropy of B in A.<br>
-* s_A: an estimate of the relative entropy of A in B.<br>
-
* stdev: an estimate expected per-sample standard deviation.<p>
+<tt>*</tt> lam_A: the λ values for point A.<br>
+<tt>*</tt> lam_B: the λ values for point B.<br>
+<tt>*</tt> DG: the free energy estimate.<br>
+<tt>*</tt> s_A: an estimate of the relative entropy of B in A.<br>
+<tt>*</tt> s_A: an estimate of the relative entropy of A in B.<br>
+
<tt>*</tt> stdev: an estimate expected per-sample standard deviation.<p>
The relative entropy of both states in each other's ensemble can be
interpreted as a measure of phase space overlap:
the relative entropy s_A of the work samples of lambda_B in the
ensemble of lambda_A (and vice versa for s_B), is a
measure of the 'distance' between Boltzmann distributions of
the two states, that goes to zero for identical distributions. See
-Wu & Kofke, J. Chem. Phys. 123 084109 (2009) for more information.
+Wu & Kofke, J. Chem. Phys. 123 084109 (2005) for more information.
<p>
The estimate of the expected per-sample standard deviation, as given
-in Bennett's original BAR paper:
-Bennett, J. Comp. Phys. 22, p 245 (1976), Eq. 10 gives an estimate
-of the quality of sampling (not directly of the actual statistical
-error, because it assumes independent samples).<p>
+in Bennett's original BAR paper: Bennett, J. Comp. Phys. 22, p 245 (1976).
+Eq. 10 therein gives an estimate of the quality of sampling (not directly
+of the actual statistical error, because it assumes independent samples).<p>
+To get a visual estimate of the phase space overlap, use the
+<tt>-oh</tt> option to write series of histograms, together with the
+<tt>-nbin</tt> option.<p>
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dhdl.xvg</a></tt> </TD><TD> Input, Opt., Mult. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html"> ener.edr</a></tt> </TD><TD> Input, Opt., Mult. </TD><TD> Energy file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> bar.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> barint.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">histogram.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html"> energy.edr</a></tt> </TD><TD> Input, Opt., Mult. </TD><TD> Energy file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Begin time for BAR </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> End time for BAR </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nbmin</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>5</tt> </TD><TD> Minimum number of blocks for error estimation </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nbmax</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>5</tt> </TD><TD> Maximum number of blocks for error estimation </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nbin</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Number of bins for histogram output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]extp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Whether to linearly extrapolate dH/dl values to use as energies </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_bond makes a distribution of bond lengths. If all is well a
-gaussian distribution should be made when using a harmonic potential.
+<tt>g_bond</tt> makes a distribution of bond lengths. If all is well a
+Gaussian distribution should be made when using a harmonic potential.
Bonds are read from a single group in the index file in order i1-j1
i2-j2 through in-jn.<p>
<tt>-tol</tt> gives the half-width of the distribution as a fraction
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-blen</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Bond length. By default length of first bond </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Half width of distribution as fraction of blen </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average bond length distributions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]averdist</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average distances (turns on -d) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Half width of distribution as fraction of <tt>-blen</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average bond length distributions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]averdist</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average distances (turns on <tt>-d</tt>) </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bundle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_bundle analyzes bundles of axes. The axes can be for instance
+<tt>g_bundle</tt> analyzes bundles of axes. The axes can be for instance
helix axes. The program reads two index groups and divides both
of them in <tt>-na</tt> parts. The centers of mass of these parts
define the tops and bottoms of the axes.
<p>
With option <tt>-oa</tt> the <a href="top.html">top</a>, mid (or kink when <tt>-ok</tt> is set)
and bottom points of each axis
-are written to a <a href="pdb.html">pdb</a> file each frame. The residue numbers correspond
-to the axis numbers. When viewing this file with <tt>rasmol</tt>, use the
+are written to a <tt>.<a href="pdb.html">pdb</a></tt> file each frame. The residue numbers correspond
+to the axis numbers. When viewing this file with Rasmol, use the
command line option <tt>-nmrpdb</tt>, and type <tt>set axis true</tt> to
display the reference axis.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-na</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of axes </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the Z-axis as reference iso the average axis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the <it>z</it>-axis as reference instead of the average axis </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_chi</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_chi computes phi, psi, omega and chi dihedrals for all your
+<tt>g_chi</tt> computes φ, ψ, ω, and χ dihedrals for all your
amino acid backbone and sidechains.
It can compute dihedral angle as a function of time, and as
histogram distributions.
-The distributions
(histo-(dihedral)(RESIDUE).<a href="xvg.html">xvg</a>) are cumulative over all residues of each type.<p>
+The distributions
<tt>(histo-(dihedral)(RESIDUE).<a href="xvg.html">xvg</a></tt>) are cumulative over all residues of each type.<p>
If option <tt>-corr</tt> is given, the program will
calculate dihedral autocorrelation functions. The function used
-is C(t) = < cos(chi(tau)) cos(chi(tau+t)) >. The use of cosines
+is C(t) = <cos(χ(τ)) cos(χ(τ+t))>. The use of cosines
rather than angles themselves, resolves the problem of periodicity.
-(Van der Spoel & Berendsen (1997), <b>Biophys. J. 72</b>, 2032-2041).
+(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).
Separate files for each dihedral of each residue
-(corr(dihedral)(RESIDUE)(nresnr).<a href="xvg.html">xvg</a>) are output, as well as a
+<tt>(corr(dihedral)(RESIDUE)(nresnr).<a href="xvg.html">xvg</a></tt>) are output, as well as a
file containing the information for all residues (argument of <tt>-corr</tt>).<p>
With option <tt>-all</tt>, the angles themselves as a function of time for
-each residue are printed to separate files (dihedral)(RESIDUE)(nresnr).<a href="xvg.html">xvg</a>.
+each residue are printed to separate files <tt>(dihedral)(RESIDUE)(nresnr).<a href="xvg.html">xvg</a></tt>.
These can be in radians or degrees.<p>
A <a href="log.html">log</a> file (argument <tt>-g</tt>) is also written. This contains <br>
(a) information about the number of residues of each type.<br>
-(b) The NMR 3J coupling constants from the Karplus equation.<br>
+(b) The NMR ^3J coupling constants from the Karplus equation.<br>
(c) a table for each residue of the number of transitions between
-rotamers per nanosecond, and the order parameter S2 of each dihedral.<br>
-(d) a table for each residue of the rotamer occupancy.<br>
-All rotamers are taken as 3-fold, except for omegas and chi-dihedrals
-to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu
-and gln, and chi4 of arg), which are 2-fold. "rotamer 0" means
+rotamers per nanosecond, and the order parameter S^2 of each dihedral.<br>
+(d) a table for each residue of the rotamer occupancy.<p>
+All rotamers are taken as 3-fold, except for ω and χ dihedrals
+to planar groups (i.e. χ_2 of aromatics, Asp and Asn; χ_3 of Glu
+and Gln; and χ_4 of Arg), which are 2-fold. "rotamer 0" means
that the dihedral was not in the core region of each rotamer.
The width of the core region can be set with <tt>-core_rotamer</tt><p>
-The S2 order parameters are also output to an <a href="xvg.html">xvg</a> file
-(argument <tt>-o</tt> ) and optionally as a <a href="pdb.html">pdb</a> file with
-the S2 values as B-factor (argument <tt>-p</tt>).
+The S^2 order parameters are also output to an <tt>.<a href="xvg.html">xvg</a></tt> file
+(argument <tt>-o</tt> ) and optionally as a <tt>.<a href="pdb.html">pdb</a></tt> file with
+the S^2 values as B-factor (argument <tt>-p</tt>).
The total number of rotamer transitions per timestep
(argument <tt>-ot</tt>), the number of transitions per rotamer
-(argument <tt>-rt</tt>), and the 3J couplings (argument <tt>-jc</tt>),
-can also be written to .<a href="xvg.html">xvg</a> files.<p>
-If <tt>-chi_prod</tt> is set (and maxchi > 0), cumulative rotamers, e.g.
-1+9(chi1-1)+3(chi2-1)+(chi3-1) (if the residue has three 3-fold
-dihedrals and maxchi >= 3)
+(argument <tt>-rt</tt>), and the ^3J couplings (argument <tt>-jc</tt>),
+can also be written to <tt>.<a href="xvg.html">xvg</a></tt> files. Note that the analysis
+of rotamer transitions assumes that the supplied trajectory frames
+are equally spaced in time.<p>
+If <tt>-chi_prod</tt> is set (and <tt>-maxchi</tt> > 0), cumulative rotamers, e.g.
+1+9(χ_1-1)+3(χ_2-1)+(χ_3-1) (if the residue has three 3-fold
+dihedrals and <tt>-maxchi</tt> >= 3)
are calculated. As before, if any dihedral is not in the core region,
the rotamer is taken to be 0. The occupancies of these cumulative
rotamers (starting with rotamer 0) are written to the file
that is the argument of <tt>-cp</tt>, and if the <tt>-all</tt> flag
is given, the rotamers as functions of time
-are written to chiproduct(RESIDUE)(nresnr).<a href="xvg.html">xvg</a>
-and their occupancies to
histo-chiproduct(RESIDUE)(nresnr).<a href="xvg.html">xvg</a>.<p>
-The option <tt>-r</tt> generates a contour plot of the average omega angle
-as a function of the phi and psi angles, that is, in a Ramachandran plot
-the average omega angle is plotted using color coding.
+are written to <tt>chiproduct(RESIDUE)(nresnr).<a href="xvg.html">xvg</a></tt>
+and their occupancies to
<tt>histo-chiproduct(RESIDUE)(nresnr).<a href="xvg.html">xvg</a></tt>.<p>
+The option <tt>-r</tt> generates a contour plot of the average ω angle
+as a function of the φ and ψ angles, that is, in a Ramachandran plot
+the average ω angle is plotted using color coding.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> starting residue </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for Phi dihedral angles </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]psi</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for Psi dihedral angles </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]omega</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for Omega dihedrals (peptide bonds) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rama</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate Phi/Psi and Chi1/Chi2 ramachandran plots </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]viol</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write a file that gives 0 or 1 for violated Ramachandran angles </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]periodic</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print dihedral angles modulo 360 degrees </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output separate files for every dihedral. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rad</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> in angle vs time files, use radians rather than degrees. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]shift</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute chemical shifts from Phi/Psi angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for φ dihedral angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]psi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for ψ dihedral angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]omega</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for ω dihedrals (peptide bonds) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rama</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate φ/ψ and χ_1/χ_2 Ramachandran plots </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]viol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write a file that gives 0 or 1 for violated Ramachandran angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]periodic</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print dihedral angles modulo 360 degrees </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output separate files for every dihedral. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rad</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> in angle vs time files, use radians rather than degrees. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]shift</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute chemical shifts from φ/ψ angles </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-binwidth</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> bin width for histograms (degrees) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-core_rotamer</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> only the central -core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-maxchi</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> calculate first ndih Chi dihedrals: <tt>0</tt>, <tt>1</tt>, <tt>2</tt>, <tt>3</tt>, <tt>4</tt>, <tt>5</tt> or <tt>6</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normhisto</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize histograms </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ramomega</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> compute average omega as a function of phi/psi and plot it in an <a href="xpm.html">xpm</a> plot </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bfact</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> B-factor value for <a href="pdb.html">pdb</a> file for atoms with no calculated dihedral order parameter </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]chi_prod</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> compute a single cumulative rotamer for each residue </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]HChi</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Include dihedrals to sidechain hydrogens </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. -bmax <= 0 means no limit. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-core_rotamer</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> only the central <tt>-core_rotamer</tt>*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxchi</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> calculate first ndih χ dihedrals: <tt>0</tt>, <tt>1</tt>, <tt>2</tt>, <tt>3</tt>, <tt>4</tt>, <tt>5</tt> or <tt>6</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normhisto</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize histograms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ramomega</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> compute average omega as a function of φ/ψ and plot it in an <tt>.<a href="xpm.html">xpm</a></tt> plot </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bfact</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> B-factor value for <tt>.<a href="pdb.html">pdb</a></tt> file for atoms with no calculated dihedral order parameter </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]chi_prod</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> compute a single cumulative rotamer for each residue </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]HChi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Include dihedrals to sidechain hydrogens </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. <tt>-bmax</tt> <= 0 means no limit. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<H3>Known problems</H3>
<UL>
<LI>Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.
-<LI>Phi and psi dihedrals are calculated in a non-standard way, using H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like <a href="g_rama.html">g_rama</a>.
-<LI>-r0 option does not work properly
-<LI>Rotamers with multiplicity 2 are printed in chi.<a href="log.html">log</a> as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0
+<LI>φ and ψ dihedrals are calculated in a non-standard way, using H-N-CA-C for φ instead of C(-)-N-CA-C, and N-CA-C-O for ψ instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like <tt><a href="g_rama.html">g_rama</a></tt>.
+<LI><tt>-r0</tt> option does not work properly
+<LI>Rotamers with multiplicity 2 are printed in <tt>chi.<a href="log.html">log</a></tt> as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0
</UL>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_cluster</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_cluster can cluster structures with several different methods.
+<tt>g_cluster</tt> can cluster structures using several different methods.
Distances between structures can be determined from a trajectory
-or read from an XPM matrix file with the <tt>-dm</tt> option.
+or read from an <tt>.<a href="xpm.html">xpm</a></tt> matrix file with the <tt>-dm</tt> option.
RMS deviation after fitting or RMS deviation of atom-pair distances
can be used to define the distance between structures.<p>
single linkage: add a structure to a cluster when its distance to any
(<it>Angew. Chem. Int. Ed.</it> <b>1999</b>, <it>38</it>, pp 236-240).
Count number of neighbors using cut-off, take structure with
largest number of neighbors with all its neighbors as cluster
-and eleminate it from the pool of clusters. Repeat for remaining
+and eliminate it from the pool of clusters. Repeat for remaining
structures in pool.<p>
When the clustering algorithm assigns each structure to exactly one
cluster (single linkage, Jarvis Patrick and gromos) and a trajectory
<tt>-cl</tt> writes average (with option <tt>-av</tt>) or central
structure of each cluster or writes numbered files with cluster members
for a selected set of clusters (with option <tt>-wcl</tt>, depends on
-<tt>-nst</tt> and <tt>-rmsmin</tt>).<br>
+<tt>-nst</tt> and <tt>-rmsmin</tt>). The center of a cluster is the
+structure with the smallest average RMSD from all other structures
+of the cluster.<br>
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]dista</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use RMSD of distances instead of RMS deviation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize RMSD matrix in # levels </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]dista</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use RMSD of distances instead of RMS deviation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize RMSD matrix in this number of levels </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> RMSD cut-off (nm) for two structures to be neighbor </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use least squares fitting before RMSD calculation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use least squares fitting before RMSD calculation </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum level in RMSD matrix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyze every nr-th frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]av</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write average iso middle structure for each cluster </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-wcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Write all structures for first # clusters to numbered files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nst</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write all structures if more than # per cluster </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]av</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write average iso middle structure for each cluster </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-wcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Write the structures for this number of clusters to numbered files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nst</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write all structures if more than this number of structures per cluster </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rmsmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> minimum rms difference with rest of cluster for writing structures </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-method</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>linkage</tt> </TD><TD> Method for cluster determination: <tt>linkage</tt>, <tt>jarvis-patrick</tt>, <tt>monte-carlo</tt>, <tt>diagonalization</tt> or <tt>gromos</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-minstruct</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Minimum number of structures in cluster for coloring in the <a href="xpm.html">xpm</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]binary</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-minstruct</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Minimum number of structures in cluster for coloring in the <tt>.<a href="xpm.html">xpm</a></tt> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]binary</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by <tt>-cutoff</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-M</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of identical nearest neighbors required to form a cluster </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1993</tt> </TD><TD> Random number seed for Monte Carlo clustering algorithm </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-niter</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10000</tt> </TD><TD> Number of iterations for MC </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-kT</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> PBC check </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_clustsize</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
This program computes the size distributions of molecular/atomic clusters in
-the gas phase. The output is given in the form of a XPM file.
-The total number of clusters is written to a
XVG file.<p>
+the gas phase. The output is given in the form of an <tt>.<a href="xpm.html">xpm</a></tt> file.
+The total number of clusters is written to a
n <tt>.<a href="xvg.html">xvg</a></tt> file.<p>
When the <tt>-mol</tt> option is given clusters will be made out of
molecules rather than atoms, which allows clustering of large molecules.
In this case an index file would still contain atom numbers
or your calculation will die with a SEGV.<p>
When velocities are present in your trajectory, the temperature of
-the largest cluster will be printed in a separate <a href="xvg.html">xvg</a> file assuming
+the largest cluster will be printed in a separate <tt>.<a href="xvg.html">xvg</a></tt> file assuming
that the particles are free to move. If you are using constraints,
please correct the temperature. For instance water simulated with SHAKE
or SETTLE will yield a temperature that is 1.5 times too low. You can
-compensate for this with the -ndf option. Remember to take the removal
+compensate for this with the <tt>-ndf</tt> option. Remember to take the removal
of center of mass motion into account.<p>
The <tt>-mc</tt> option will produce an index file containing the
atom numbers of the largest cluster.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.35 </tt> </TD><TD> Largest distance (nm) to be considered in a cluster </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Cluster molecules rather than atoms (needs <a href="tpr.html">tpr</a> file) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Cluster molecules rather than atoms (needs <tt>.<a href="tpr.html">tpr</a></tt> file) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of frames to skip between writing </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of levels of grey in <a href="xpm.html">xpm</a> output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of levels of grey in <tt>.<a href="xpm.html">xpm</a></tt> output </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ndf</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rgblo</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 0</tt> </TD><TD> RGB values for the color of the lowest occupied cluster size </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rgbhi</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 1</tt> </TD><TD> RGB values for the color of the highest occupied cluster size </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_confrms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_confrms computes the root mean square deviation (RMSD) of two
-structures after LSQ fitting the second structure on the first one.
+<tt>g_confrms</tt> computes the root mean square deviation (RMSD) of two
+structures after least-squares fitting the second structure on the first one.
The two structures do NOT need to have the same number of atoms,
only the two index groups used for the fit need to be identical.
With <tt>-name</tt> only matching atom names from the selected groups
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only write the fitted structure to file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Mass-weighted fitting and RMSD </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Try to make molecules whole again </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do least squares superposition of the target structure to the reference </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]name</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only compare matching atom names </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]label</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Added chain labels A for first and B for second structure </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]bfac</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output B-factors from atomic MSD values </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only write the fitted structure to file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Mass-weighted fitting and RMSD </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Try to make molecules whole again </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do least squares superposition of the target structure to the reference </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]name</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only compare matching atom names </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]label</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Added chain labels A for first and B for second structure </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]bfac</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output B-factors from atomic MSD values </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_covar</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
Option <tt>-ascii</tt> writes the whole covariance matrix to
an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
<p>
-Option <tt>-<a href="xpm.html">xpm</a></tt> writes the whole covariance matrix to an <a href="xpm.html">xpm</a> file.
+Option <tt>-<a href="xpm.html">xpm</a></tt> writes the whole covariance matrix to an <tt>.<a href="xpm.html">xpm</a></tt> file.
<p>
-Option <tt>-xpma</tt> writes the atomic covariance matrix to an <a href="xpm.html">xpm</a> file,
+Option <tt>-xpma</tt> writes the atomic covariance matrix to an <tt>.<a href="xpm.html">xpm</a></tt> file,
i.e. for each atom pair the sum of the xx, yy and zz covariances is
written.
+<p>
+Note that the diagonalization of a matrix requires memory and time
+that will increase at least as fast as than the square of the number
+of atoms involved. It is easy to run out of memory, in which
+case this tool will probably exit with a 'Segmentation fault'. You
+should consider carefully whether a reduced set of atoms will meet
+your needs for lower costs.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Fit to a reference structure </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ref</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the deviation from the conformation in the structure file instead of from the average </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mwa</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Mass-weighted covariance analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Fit to a reference structure </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ref</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the deviation from the conformation in the structure file instead of from the average </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mwa</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Mass-weighted covariance analysis </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Last eigenvector to write away (-1 is till the last) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Apply corrections for periodic boundary conditions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Apply corrections for periodic boundary conditions </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_current</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-This is a tool for calculating the current autocorrelation function, the correlation
+<tt>g_current</tt> is a tool for calculating the current autocorrelation function, the correlation
of the rotational and translational dipole moment of the system, and the resulting static
-dielectric constant. To obtain a reasonable result the index group has to be neutral.
-Furthermore the routine is capable of extracting the static conductivity from the current
-autocorrelation function, if velocities are given. Additionally an Einstein-Helfand fit also
-
allows to get the static conductivity.<p>
+dielectric constant. To obtain a reasonable result, the index group has to be neutral.
+Furthermore, the routine is capable of extracting the static conductivity from the current
+autocorrelation function, if velocities are given. Additionally, an Einstein-Helfand fit
+
can be used to obtain the static conductivity.<p>
The flag <tt>-caf</tt> is for the output of the current autocorrelation function and <tt>-mc</tt> writes the
correlation of the rotational and translational part of the dipole moment in the corresponding
-file. However this option is only available for trajectories containing velocities.
+file. However, this option is only available for trajectories containing velocities.
Options <tt>-sh</tt> and <tt>-tr</tt> are responsible for the averaging and integration of the
autocorrelation functions. Since averaging proceeds by shifting the starting point
through the trajectory, the shift can be modified with <tt>-sh</tt> to enable the choice of uncorrelated
Option <tt>-temp</tt> sets the temperature required for the computation of the static dielectric constant.
<p>
Option <tt>-<a href="eps.html">eps</a></tt> controls the dielectric constant of the surrounding medium for simulations using
-a Reaction Field or dipole corrections of the Ewald summation (<a href="eps.html">eps</a>=0 corresponds to
+a Reaction Field or dipole corrections of the Ewald summation (<tt>-<a href="eps.html">eps</a></tt>=0 corresponds to
tin-foil boundary conditions).
<p>
<tt>-[no]nojump</tt> unfolds the coordinates to allow free diffusion. This is required to get a continuous
-translational dipole moment, required for the Einstein-Helfand fit. The resuls from the fit allow to
-determine the dielectric constant for system of charged molecules. However it is also possible to extract
+translational dipole moment, required for the Einstein-Helfand fit. The results from the fit allow
+the determination of the dielectric constant for system of charged molecules. However, it is also possible to extract
the dielectric constant from the fluctuations of the total dipole moment in folded coordinates. But this
-options has to be used with care, since only very short time spans fulfill the approximation, that the density
+option has to be used with care, since only very short time spans fulfill the approximation that the density
of the molecules is approximately constant and the averages are already converged. To be on the safe side,
the dielectric constant should be calculated with the help of the Einstein-Helfand method for
the translational part of the dielectric constant.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-sh</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1000</tt> </TD><TD> Shift of the frames for averaging the correlation functions and the mean-square displacement. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Removes jumps of atoms across the box. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eps</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Dielectric constant of the surrounding medium. <a href="eps.html">eps</a>=0.0 corresponds to <a href="eps.html">eps</a>=infinity (thinfoil boundary conditions). </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Removes jumps of atoms across the box. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eps</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Dielectric constant of the surrounding medium. The value zero corresponds to infinity (tin-foil boundary conditions). </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>100 </tt> </TD><TD> Begin of the fit of the straight line to the MSD of the translational fraction of the dipole moment. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-efit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400 </tt> </TD><TD> End of the fit of the straight line to the MSD of the translational fraction of the dipole moment. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bvit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> Begin of the fit of the current autocorrelation function to a*t^b. </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_density</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-Compute partial densities across the box, using an index file. Densities
-in kg/m^3, number densities or electron densities can be
+Compute partial densities across the box, using an index file.<p>
+For the total density of NPT simulations, use <tt><a href="g_energy.html">g_energy</a></tt> instead.
+<p>
+Densities are in kg/m^3, and number densities or electron densities can also be
calculated. For electron densities, a file describing the number of
electrons for each type of atom should be provided using <tt>-ei</tt>.
It should look like:<br>
- 2<br>
- atomname = nrelectrons<br>
- atomname = nrelectrons<br>
+ <tt>2</tt><br>
+ <tt>atomname = nrelectrons</tt><br>
+ <tt>atomname = nrelectrons</tt><br>
The first line contains the number of lines to read from the file.
There should be one line for each unique atom name in your system.
The number of electrons for each atom is modified by its atomic
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>50</tt> </TD><TD> Divide the box in #nr slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>50</tt> </TD><TD> Divide the box in this number of slices. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dens</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>mass</tt> </TD><TD> Density: <tt>mass</tt>, <tt>number</tt>, <tt>charge</tt> or <tt>electron</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to compute densities of </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]symm</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Symmetrize the density along the axis, with respect to the center. Useful for bilayers. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]center</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups of which to compute densities. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]symm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Symmetrize the density along the axis, with respect to the center. Useful for bilayers. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]center</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0. </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_densmap</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_densmap computes 2D number-density maps.
+<tt>g_densmap</tt> computes 2D number-density maps.
It can make planar and axial-radial density maps.
The output <tt>.<a href="xpm.html">xpm</a></tt> file can be visualized with for instance xv
-and can be converted to postscript with <a href="xpm2ps.html">xpm2ps</a>.
-Optionally, output can be in text form to a .<a href="dat.html">dat</a> file.
+and can be converted to postscript with <tt><a href="xpm2ps.html">xpm2ps</a></tt>.
+Optionally, output can be in text form to a <tt>.<a href="dat.html">dat</a></tt> file with <tt>-od</tt>, instead of the usual <tt>.<a href="xpm.html">xpm</a></tt> file with <tt>-o</tt>.
<p>
The default analysis is a 2-D number-density <a href="map.html">map</a> for a selected
group of atoms in the x-y plane.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02 </tt> </TD><TD> Grid size (nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-aver</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> The direction to average over: <tt>z</tt>, <tt>y</tt> or <tt>x</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Minimum coordinate for averaging </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-n2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of grid cells in the second direction </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-amax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum axial distance from the center </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum radial distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mirror</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Add the mirror image below the axial axis </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sums</tt></b> </TD><TD ALIGN=RIGHT>
gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print density sums (1D <a href="map.html">map</a>) to stdout </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mirror</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Add the mirror image below the axial axis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sums</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print density sums (1D <a href="map.html">map</a>) to stdout </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-unit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>nm-3</tt> </TD><TD> Unit for the output: <tt>nm-3</tt>, <tt>nm-2</tt> or <tt>count</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum density in output </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum density in output (0 means calculate it) </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_densorder</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5.4-dev-20110404-3c0e5ec<br>
-Mon 4 Apr 2011</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dielectric</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-dielectric calculates frequency dependent dielectric constants
+<tt>g_dielectric</tt> calculates frequency dependent dielectric constants
from the autocorrelation function of the total dipole moment in
-your simulation. This ACF can be generated by <a href="g_dipoles.html">g_dipoles</a>.
-For an estimate of the error you can run g_statistics on the
-ACF, and use the output thus generated for this program.
+your simulation. This ACF can be generated by <tt><a href="g_dipoles.html">g_dipoles</a></tt>.
The functional forms of the available functions are:<p>
-One parameter : y = Exp[-a1 x],
-Two parameters : y = a2 Exp[-a1 x],
-Three parameters: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x].
+One parameter: y = exp(-a_1 x),<br>
+Two parameters: y = a_2 exp(-a_1 x),<br>
+Three parameters: y = a_2 exp(-a_1 x) + (1 - a_2) exp(-a_3 x).<br>
Start values for the fit procedure can be given on the command line.
-It is also possible to fix parameters at their start value, use -fix
+It is also possible to fix parameters at their start value, use <tt>-fix</tt>
with the number of the parameter you want to fix.
<p>
Three output files are generated, the first contains the ACF,
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fft</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> use fast fourier transform for correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]x1</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> use first column as X axis rather than first data set </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eint</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Time were to end the integration of the data and start to use the fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fft</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> use fast fourier transform for correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]x1</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> use first column as <it>x</it>-axis rather than first data set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eint</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Time to end the integration of the data and start to use the fit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Begin time of fit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-efit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>500 </tt> </TD><TD> End time of fit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>500 </tt> </TD><TD> Length of function including data and tail from fit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-A</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> Start value for fit parameter A </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tau1</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>10 </tt> </TD><TD> Start value for fit parameter tau1 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tau2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Start value for fit parameter tau2 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eps0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>80 </tt> </TD><TD> Epsilon 0 of your liquid </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-epsRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>78.5 </tt> </TD><TD> Epsilon of the reaction field used in your simulation. A value of 0 means infinity. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tau1</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>10 </tt> </TD><TD> Start value for fit parameter τ1 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tau2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Start value for fit parameter τ2 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eps0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>80 </tt> </TD><TD> ε0 of your liquid </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-epsRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>78.5 </tt> </TD><TD> ε of the reaction field used in your simulation. A value of 0 means infinity. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fix</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Fix parameters at their start values, A (2), tau1 (1), or tau2 (4) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ffn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ffn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nsmooth</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of points for smoothing </TD></TD>
</TABLE>
<P>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dipoles</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_dipoles computes the total dipole plus fluctuations of a simulation
+<tt>g_dipoles</tt> computes the total dipole plus fluctuations of a simulation
system. From this you can compute e.g. the dielectric constant for
-low dielectric media.
+low-dielectric media.
For molecules with a net charge, the net charge is subtracted at
center of mass of the molecule.<p>
-The file Mtot.<a href="xvg.html">xvg</a> contains the total dipole moment of a frame, the
+The file <tt>Mtot.<a href="xvg.html">xvg</a></tt> contains the total dipole moment of a frame, the
components as well as the norm of the vector.
-The file aver.<a href="xvg.html">xvg</a> contains < |Mu|^2 > and |< Mu >|^2 during the
+The file <tt>aver.<a href="xvg.html">xvg</a></tt> contains <|μ|^2> and |<μ>|^2 during the
simulation.
-The file dipdist.<a href="xvg.html">xvg</a> contains the distribution of dipole moments during
+The file <tt>dipdist.<a href="xvg.html">xvg</a></tt> contains the distribution of dipole moments during
the simulation
-The
mu_max is used as the highest value in the distribution graph.<p>
-Furthermore the dipole autocorrelation function will be computed when
-option -corr is used. The output file name is given with the <tt>-c</tt>
+The
value of <tt>-mumax</tt> is used as the highest value in the distribution graph.<p>
+Furthermore, the dipole autocorrelation function will be computed when
+option <tt>-corr</tt> is used. The output file name is given with the <tt>-c</tt>
option.
The correlation functions can be averaged over all molecules
(<tt>mol</tt>), plotted per molecule separately (<tt>molsep</tt>)
Option <tt>-g</tt> produces a plot of the distance dependent Kirkwood
G-factor, as well as the average cosine of the angle between the dipoles
as a function of the distance. The plot also includes gOO and hOO
-according to Nymand & Linse, JCP 112 (2000) pp 6386-6395. In the same plot
+according to Nymand & Linse, J. Chem. Phys. 112 (2000) pp 6386-6395. In the same plot,
we also include the energy per scale computed by taking the inner product of
the dipoles divided by the distance to the third power.<p>
<p>
EXAMPLES<p>
-
g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft<p>
+
<tt>g_dipoles -corr mol -P 1 -o dip_sqr -mu 2.273 -mumax 5.0</tt><p>
This will calculate the autocorrelation function of the molecular
dipoles using a first order Legendre polynomial of the angle of the
dipole vector and itself a time t later. For this calculation 1001
-frames will be used. Further the dielectric constant will be calculated
-using an epsilonRF of infinity (default), temperature of 300 K (default) and
+frames will be used. Further, the dielectric constant will be calculated
+using an <tt>-epsilonRF</tt> of infinity (default), temperature of 300 K (default) and
an average dipole moment of the molecule of 2.273 (SPC). For the
distribution function a maximum of 5.0 will be used.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-mu</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> dipole of a single molecule (in Debye) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-mumax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> max dipole in Debye (for histrogram) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-epsilonRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mumax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> max dipole in Debye (for histogram) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-epsilonRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> ε of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip steps in the output (but not in the computations) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Average temperature of the simulation (needed for dielectric constant calculation) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-corr</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Correlation function to calculate: <tt>none</tt>, <tt>mol</tt>, <tt>molsep</tt> or <tt>total</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Calculate |cos theta| between all pairs of molecules. May be slow </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncos</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Must be 1 or 2. Determines whether the <cos> is computed between all mole cules in one group, or between molecules in two different groups. This turns on the -gkr flag. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Calculate |cos(θ)| between all pairs of molecules. May be slow </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncos</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Must be 1 or 2. Determines whether the <cos(θ)> is computed between all molecules in one group, or between molecules in two different groups. This turns on the <tt>-g</tt> flag. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-axis</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the computational box in direction X, Y or Z. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Divide the box in #nr slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Divide the box into this number of slices. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-gkratom</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Use the n-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-gkratom2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rcmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the <a href="xpm.html">xpm</a> file from the -cmap option. By default the cosine of the angle between the dipoles is plotted. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rcmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterion based on the box length will be used. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the <tt>.<a href="xpm.html">xpm</a></tt> file from the <tt>-cmap</tt> option. By default the cosine of the angle between the dipoles is plotted. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of colors in the cmap output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ndegrees</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>90</tt> </TD><TD> Number of divisions on the y-axis in the camp output (for 180 degrees) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ndegrees</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>90</tt> </TD><TD> Number of divisions on the <it>y</it>-axis in the cmap output (for 180 degrees) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_disre</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_disre computes violations of distance restraints.
-If necessary all protons can be added to a protein molecule
-using the <
a href="protonate.html">protonate</a> program.<p>
+<tt>g_disre</tt> computes violations of distance restraints.
+If necessary, all protons can be added to a protein molecule
+using the <
tt>g_<a href="protonate.html">protonate</a></tt> program.<p>
The program always
computes the instantaneous violations rather than time-averaged,
because this analysis is done from a trajectory file afterwards
the time averaged values per restraint are given in the <a href="log.html">log</a> file.<p>
An index file may be used to select specific restraints for
printing.<p>
-When the optional<tt>-q</tt> flag is given a <a href="pdb.html">pdb</a> file coloured by the
+When the optional <tt>-q</tt> flag is given a <tt>.<a href="pdb.html">pdb</a></tt> file coloured by the
amount of average violations.<p>
When the <tt>-c</tt> option is given, an index file will be read
containing the frames in your trajectory corresponding to the clusters
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ntop</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of large violations that are stored in the <a href="log.html">log</a> file every step </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-maxdr</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of levels in the matrix output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]third</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use inverse third power averaging or linear for matrix output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]third</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use inverse third power averaging or linear for matrix output </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_dist can calculate the distance between the centers of mass of two
+<tt>g_dist</tt> can calculate the distance between the centers of mass of two
groups of atoms as a function of time. The total distance and its
-
x, y and z components are plotted.<p>
+
<it>x</it>-, <it>y</it>-, and <it>z</it>-components are plotted.<p>
Or when <tt>-dist</tt> is set, print all the atoms in group 2 that are
closer than a certain distance to the center of mass of group 1.<p>
With options <tt>-lt</tt> and <tt>-dist</tt> the number of contacts
of all atoms in group 2 that are closer than a certain distance
to the center of mass of group 1 are plotted as a function of the time
-that the contact was continously present.<p>
+that the contact was continuously present. The <tt>-intra</tt> switch enables
+calculations of intramolecular distances avoiding distance calculation to its
+periodic images. For a proper function, the molecule in the input trajectory
+should be whole (e.g. by preprocessing with <tt><a href="trjconv.html">trjconv</a> -pbc</tt>) or a matching
+topology should be provided. The <tt>-intra</tt> switch will only give
+meaningful results for intramolecular and not intermolecular distances.<p>
Other programs that calculate distances are <tt><a href="g_mindist.html">g_mindist</a></tt>
and <tt><a href="g_bond.html">g_bond</a></tt>.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]intra</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate distances without considering periodic boundaries, e.g. intramolecular. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Print all atoms in group 2 closer than dist to the center of mass of group 1 </TD></TD>
</TABLE>
<P>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>g_dos</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
+<TABLE WIDTH="98%" NOBORDER >
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
+<TD WIDTH=116>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dos</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
+<HR>
+<H3>Description</H3>
+<p>
+<tt>g_dos</tt> computes the Density of States from a simulations.
+In order for this to be meaningful the velocities must be saved
+in the trajecotry with sufficiently high frequency such as to cover
+all vibrations. For flexible systems that would be around a few fs
+between saving. Properties based on the DoS are printed on the
+standard output.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-vacf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> vacf.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mvacf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> mvacf.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dos</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dos.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> dos.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Be loud and noisy. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]recip</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use cm^-1 on X-axis instead of 1/ps for DoS plots. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]abs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normdos</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature in the simulation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
+</TABLE>
+<P>
+<H3>Known problems</H3>
+<UL>
+<LI>This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision).
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>g_dyecoupl</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
+<TABLE WIDTH="98%" NOBORDER >
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
+<TD WIDTH=116>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dyecoupl</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
+<HR>
+<H3>Description</H3>
+<p>
+This tool extracts dye dynamics from trajectory files.
+Currently, R and kappa^2 between dyes is extracted for (F)RET
+simulations with assumed dipolar coupling as in the Foerster equation.
+It further allows the calculation of R(t) and kappa^2(t), R and
+kappa^2 histograms and averages, as well as the instantaneous FRET
+efficiency E(t) for a specified Foerster radius R_0 (switch <tt>-R0</tt>).
+The input dyes have to be whole (see res and mol pbc options
+in <tt><a href="trjconv.html">trjconv</a></tt>).
+The dye transition dipole moment has to be defined by at least
+a single atom pair, however multiple atom pairs can be provided
+in the index file. The distance R is calculated on the basis of
+the COMs of the given atom pairs.
+The <tt>-pbcdist</tt> option calculates distances to the nearest periodic
+image instead to the distance in the box. This works however only,for periodic boundaries in all 3 dimensions.
+The <tt>-norm</tt> option (area-) normalizes the histograms.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rkappa.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oe</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> insteff.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> rkappa.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rhist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rhist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-khist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> khist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbcdist</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Distance R based on PBC </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Normalize histograms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bins</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>50</tt> </TD><TD> # of histogram bins </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-R0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Foerster radius including kappa^2=2/3 in nm </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dyndom</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_dyndom reads a <a href="pdb.html">pdb</a> file output from DynDom
-http://www.cmp.uea.ac.uk/dyndom/
-It reads the coordinates, and the coordinates of the rotation axis
-furthermore it reads an index file containing the domains.
-Furthermore it takes the first and last atom of the arrow file
+<tt>g_dyndom</tt> reads a <tt>.<a href="pdb.html">pdb</a></tt> file output from DynDom
+(http://www.cmp.uea.ac.uk/dyndom/).
+It reads the coordinates, the coordinates of the rotation axis,
+and an index file containing the domains.
+Furthermore, it takes the first and last atom of the arrow file
as command line arguments (head and tail) and
finally it takes the translation vector (given in DynDom info file)
and the angle of rotation (also as command line arguments). If the angle
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-firstangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-lastangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nframe</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>11</tt> </TD><TD> Number of steps on the pathway </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-maxangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> DymDom dtermined angle of rotation about rotation vector </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-trans</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Translation (Aangstroem) along rotation vector (see DynDom info file) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trans</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Translation (Angstrom) along rotation vector (see DynDom info file) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-head</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> First atom of the arrow vector </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Last atom of the arrow vector </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_enemat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_enemat extracts an energy matrix from the energy file (<tt>-f</tt>).
+<tt>g_enemat</tt> extracts an energy matrix from the energy file (<tt>-f</tt>).
With <tt>-groups</tt> a file must be supplied with on each
line a group of atoms to be used. For these groups matrix of
interaction energies will be extracted from the energy file
by looking for energy groups with names corresponding to pairs
-of groups of atoms. E.g. if your <tt>-groups</tt> file contains:<br>
+of groups of atoms, e.g. if your <tt>-groups</tt> file contains:<br>
<tt>2</tt><br>
<tt>Protein</tt><br>
<tt>SOL</tt><br>
Finally, the total interaction energy energy per group can be
calculated (<tt>-etot</tt>).<p>
An approximation of the free energy can be calculated using:
-E(free) = E0 + kT <a href="log.html">log</a>( <exp((E-E0)/kT)> ), where '<>'
+E_free = E_0 + kT <a href="log.html">log</a>(<exp((E-E_0)/kT)>), where '<>'
stands for time-average. A file with reference free energies
can be supplied to calculate the free energy difference
with some reference state. Group names (e.g. residue names)
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip number of frames between data points </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mean</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> with -groups extracts matrix of mean energies instead of matrix for each timestep </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mean</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> with <tt>-groups</tt> extracts matrix of mean energies instead of matrix for each timestep </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> number of levels for matrix colors </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1e+20 </tt> </TD><TD> max value for energies </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1e+20</tt> </TD><TD> min value for energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> extract Coulomb SR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]coulr</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Coulomb LR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul14</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Coulomb 1-4 energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> extract Lennard-Jones SR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Lennard-Jones LR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj14</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Lennard-Jones 1-4 energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]bhamsr</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Buckingham SR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]bhamlr</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Buckingham LR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]free</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> calculate free energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coulsr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> extract Coulomb SR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coullr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Coulomb LR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Coulomb 1-4 energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ljsr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> extract Lennard-Jones SR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ljlr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Lennard-Jones LR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Lennard-Jones 1-4 energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]bhamsr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Buckingham SR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]bhamlr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Buckingham LR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]free</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> calculate free energy </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> reference temperature for free energy calculation </TD></TD>
</TABLE>
<P>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_energy</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_energy extracts energy components or distance restraint
+<tt>g_energy</tt> extracts energy components or distance restraint
data from an energy file. The user is prompted to interactively
-select the
energy terms she wants.<p>
-Average, RMSD and drift are calculated with full precision from the
+select the
desired energy terms.<p>
+Average, RMSD, and drift are calculated with full precision from the
simulation (see printed manual). Drift is calculated by performing
-a LSQ fit of the data to a straight line. The reported total drift
+a least-squares fit of the data to a straight line. The reported total drift
is the difference of the fit at the first and last point.
An error estimate of the average is given based on a block averages
-over 5 blocks using the full precision averages. The error estimate
+over 5 blocks using the full-precision averages. The error estimate
can be performed over multiple block lengths with the options
<tt>-nbmin</tt> and <tt>-nbmax</tt>.
-Note that in most cases the energy files contains averages over all
+<b>Note</b> that in most cases the energy files contains averages over all
MD steps, or over many more points than the number of frames in
-energy file. This makes the g_energy statistics output more accurate
-than the <a href="xvg.html">xvg</a> output. When exact averages are not present in the energy
-file the statistics mentioned above is simply over the single, per-frame
+energy file. This makes the <tt>g_energy</tt> statistics output more accurate
+than the <tt>.<a href="xvg.html">xvg</a></tt> output. When exact averages are not present in the energy
+file, the statistics mentioned above are simply over the single, per-frame
energy values.<p>
-The term fluctuation gives the RMSD around the
LSQ fit.<p>
+The term fluctuation gives the RMSD around the
least-squares fit.<p>
Some fluctuation-dependent properties can be calculated provided
-the correct energy terms are selected. The following properties
+the correct energy terms are selected, and that the command line option
+<tt>-fluct_props</tt> is given. The following properties
will be computed:<br>
Property Energy terms needed<br>
---------------------------------------------------<br>
-Heat capacity Cp (NPT sims): Enthalpy, Temp <br>
-Heat capacity Cv (NVT sims): Etot, Temp <br>
+Heat capacity C_p (NPT sims): Enthalpy, Temp <br>
+Heat capacity C_v (NVT sims): Etot, Temp <br>
Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp<br>
Isothermal compressibility: Vol, Temp <br>
Adiabatic bulk modulus: Vol, Temp <br>
---------------------------------------------------<br>
-You always need to set the number of molecules <tt>-nmol</tt>, and,
-if you used constraints in your simulations you will need to give
-the number of constraints per molecule <tt>-nconstr</tt> in order to
-correct for this: (nconstr/2) kB is subtracted from the heat
-capacity in this case. For instance in the case of rigid water
-you need to give the value 3 to this option.<p>
-When the <tt>-viol</tt> option is set, the time averaged
+You always need to set the number of molecules <tt>-nmol</tt>.
+The C_p/C_v computations do <b>not</b> include any corrections
+for quantum effects. Use the <tt>g_dos</tt> program if you need that (and you do).<p>When the <tt>-viol</tt> option is set, the time averaged
violations are plotted and the running time-averaged and
instantaneous sum of violations are recalculated. Additionally
running time-averaged and instantaneous distances between
Option <tt>-oten</tt> plots the eigenvalues of the molecular order
tensor for each orientation restraint experiment. With option
<tt>-ovec</tt> also the eigenvectors are plotted.<p>
+Option <tt>-odh</tt> extracts and plots the free energy data
+(Hamiltoian differences and/or the Hamiltonian derivative dhdl)
+from the <tt>ener.<a href="edr.html">edr</a></tt> file.<p>
With <tt>-fee</tt> an estimate is calculated for the free-energy
difference with an ideal gas state: <br>
- Delta A = A(N,V,T) - A_idgas(N,V,T) = kT ln < e^(Upot/kT) ><br>
- Delta G = G(N,p,T) - G_idgas(N,p,T) = kT ln < e^(Upot/kT) ><br>
+ Δ A = A(N,V,T) - A_idealgas(N,V,T) = kT ln(<exp(U_pot/kT)>)<br>
+ Δ G = G(N,p,T) - G_idealgas(N,p,T) = kT ln(<exp(U_pot/kT)>)<br>
where k is Boltzmann's constant, T is set by <tt>-fetemp</tt> and
the average is over the ensemble (or time in a trajectory).
Note that this is in principle
only correct when averaging over the whole (Boltzmann) ensemble
and using the potential energy. This also allows for an entropy
estimate using:<br>
- Delta S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (<Upot> - Delta A)/T<br>
- Delta S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (<Upot> + pV - Delta G)/T
+ Δ S(N,V,T) = S(N,V,T) - S_idealgas(N,V,T) = (<U_pot> - Δ A)/T<br>
+ Δ S(N,p,T) = S(N,p,T) - S_idealgas(N,p,T) = (<U_pot> + pV - Δ G)/T
<p>
When a second energy file is specified (<tt>-f2</tt>), a free energy
-difference is calculated dF = -kT ln < e ^ -(EB-EA)/kT >A ,
-where EA and EB are the energies from the first and second energy
-files, and the average is over the ensemble A. <b>NOTE</b> that
-the energies must both be calculated from the same trajectory.
-Generally, this estimate is not particularly accurate unless the
-state is very similar to the ideal gas state (i.e. the potential energies
-are very low), and more accurate free energy calculations can be performed
-using the free energy features.
+difference is calculated <br> dF = -kT ln(<exp(-(E_B-E_A)/kT)>_A) ,
+where E_A and E_B are the energies from the first and second energy
+files, and the average is over the ensemble A. The running average
+of the free energy difference is printed to a file specified by <tt>-ravg</tt>.
+<b>Note</b> that the energies must both be calculated from the same trajectory.
<P>
-<p><tt>-odh</tt>Regenerates the dhdl.xvg from the .edr file if the separate-dhdl-file
-is chosen as no in the .mdp file the .edr was generated from. This can allow more
-flexiblity in scripting as the additional dhdl.xvg file does not need to be handled
-until the analysis phase. It can also save some space by avoiding the presence of a large ASCII file.
-<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-odr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> oridevr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-odt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> oridevt.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oten</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> oriten.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-odh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-corr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> enecorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-vis</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> visco.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ravg</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">runavgdf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-odh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fee</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a free energy estimate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fee</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a free energy estimate </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fetemp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Reference temperature for free energy calculation </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-zero</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Subtract a zero-point energy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]dp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print energies in high precision </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]dp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print energies in high precision </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nbmin</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>5</tt> </TD><TD> Minimum number of blocks for error estimate </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nbmax</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>5</tt> </TD><TD> Maximum number of blocks for error estimate </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mutot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute the total dipole moment from the components </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mutot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute the total dipole moment from the components </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip number of frames between data points </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of molecules in your sample: the energies are divided by this number </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nconstr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of constraints per molecule. Necessary for calculating the heat capacity </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fluc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate autocorrelation of energy fluctuations rather than energy itself </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]orinst</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Analyse instantaneous orientation data </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ovec</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Also plot the eigenvectors with -oten </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fluct_props</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute properties based on energy fluctuations, like heat capacity </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]driftcorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Useful only for calculations of fluctuation properties. The drift in the observables will be subtracted before computing the fluctuation properties. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fluc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate autocorrelation of energy fluctuations rather than energy itself </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]orinst</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Analyse instantaneous orientation data </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ovec</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Also plot the eigenvectors with <tt>-oten</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_filter</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_filter performs frequency filtering on a trajectory.
-The filter shape is cos(pi t/A) + 1 from -A to +A, where A is given
+<tt>g_filter</tt> performs frequency filtering on a trajectory.
+The filter shape is cos(π t/A) + 1 from -A to +A, where A is given
by the option <tt>-nf</tt> times the time step in the input trajectory.
This filter reduces fluctuations with period A by 85%, with period
2*A by 50% and with period 3*A by 17% for low-pass filtering.
Both a low-pass and high-pass filtered trajectory can be written.<p>
Option <tt>-ol</tt> writes a low-pass filtered trajectory.
-A frame is written every <tt>nf</tt> input frames.
+A frame is written every <tt>-nf</tt> input frames.
This ratio of filter length and output interval ensures a good
suppression of aliasing of high-frequency motion, which is useful for
making smooth movies. Also averages of properties which are linear
Option <tt>-oh</tt> writes a high-pass filtered trajectory.
The high-pass filtered coordinates are added to the coordinates
from the structure file. When using high-pass filtering use <tt>-fit</tt>
-or make sure you use a trajectory which has been fitted on
+or make sure you use a trajectory that has been fitted on
the coordinates in the structure file.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nf</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Sets the filter length as well as the output interval for low-pass filtering </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write all low-pass filtered frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Remove jumps of atoms across the box </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Fit all frames to a reference structure </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write all low-pass filtered frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Remove jumps of atoms across the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Fit all frames to a reference structure </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_gyrate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_gyrate computes the radius of gyration of a group of atoms
-and the radii of gyration about the x, y and z axes,
+<tt>g_gyrate</tt> computes the radius of gyration of a group of atoms
+and the radii of gyration about the <it>x</it>-, <it>y</it>- and <it>z</it>-axes,
as a function of time. The atoms are explicitly mass weighted.<p>
With the <tt>-nmol</tt> option the radius of gyration will be calculated
for multiple molecules by splitting the analysis group in equally
sized parts.<p>
-With the option <tt>-nz</tt> 2D radii of gyration in the x-y plane
-of slices along the z-axis are calculated.
+With the option <tt>-nz</tt> 2D radii of gyration in the <it>x-y</it> plane
+of slices along the <it>z</it>-axis are calculated.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The number of molecules to analyze </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use absolute value of the charge of an atom as weighting factor instead of mass </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]p</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the radii of gyration about the principal axes. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]moi</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the moments of inertia (defined by the principal axes). </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nz</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Calculate the 2D radii of gyration of # slices along the z-axis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use absolute value of the charge of an atom as weighting factor instead of mass </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]p</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the radii of gyration about the principal axes. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]moi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the moments of inertia (defined by the principal axes). </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nz</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Calculate the 2D radii of gyration of this number of slices along the z-axis </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_h2order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-Compute the orientation of water molecules with respect to the normal
+<tt>g_h2order</tt> computes the orientation of water molecules with respect to the normal
of the box. The program determines the average cosine of the angle
-between de dipole moment of water and an axis of the box. The box is
+between the dipole moment of water and an axis of the box. The box is
divided in slices and the average orientation per slice is printed.
Each water molecule is assigned to a slice, per time frame, based on the
-position of the oxygen. When -nm is used the angle between the water
+position of the oxygen. When <tt>-nm</tt> is used, the angle between the water
dipole and the axis from the center of mass to the oxygen is calculated
instead of the angle between the dipole and a box axis.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Calculate order parameter as function of boxlength, dividing the box in #nr slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Calculate order parameter as function of boxlength, dividing the box in this number of slices. </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<UL>
-<LI>The program assigns whole water molecules to a slice, based on the firstatom of three in the index file group. It assumes an order O,H,H.Name is not important, but the order is. If this demand is not met,assigning molecules to slices is different.
+<LI>The program assigns whole water molecules to a slice, based on the first atom of three in the index file group. It assumes an order O,H,H. Name is not important, but the order is. If this demand is not met, assigning molecules to slices is different.
</UL>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_hbond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
-determined based on cutoffs for the angle Acceptor - Donor - Hydrogen
-(zero is extended) and the distance Hydrogen - Acceptor.
+<tt>g_hbond</tt> computes and analyzes hydrogen bonds. Hydrogen bonds are
+determined based on cutoffs for the angle Hydrogen - Donor - Acceptor
+(zero is extended) and the distance Donor - Acceptor
+(or Hydrogen - Acceptor using <tt>-noda</tt>).
OH and NH groups are regarded as donors, O is an acceptor always,
N is an acceptor by default, but this can be switched using
<tt>-nitacc</tt>. Dummy hydrogen atoms are assumed to be connected
You need to specify two groups for analysis, which must be either
identical or non-overlapping. All hydrogen bonds between the two
groups are analyzed.<p>
-If you set -shell, you will be asked for an additional index group
+If you set <tt>-shell</tt>, you will be asked for an additional index group
which should contain exactly one atom. In this case, only hydrogen
bonds between atoms within the shell distance from the one atom are
considered.<p>
+With option -ac, rate constants for hydrogen bonding can be derived with the model of Luzar and Chandler
+(Nature 394, 1996; J. Chem. Phys. 113:23, 2000) or that of Markovitz and Agmon (J. Chem. Phys 129, 2008).
+If contact kinetics are analyzed by using the -contact option, then
+n(t) can be defined as either all pairs that are not within contact distance r at time t
+(corresponding to leaving the -r2 option at the default value 0) or all pairs that
+are within distance r2 (corresponding to setting a second cut-off value with option -r2).
+See mentioned literature for more details and definitions.<p>
<tt>
[ selected ]<br>
20 21 24<br>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>30 </tt> </TD><TD> Cutoff angle (degrees, Acceptor - Donor - Hydrogen) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>30 </tt> </TD><TD> Cutoff angle (degrees, Hydrogen - Donor - Acceptor) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.35 </tt> </TD><TD> Cutoff radius (nm, X - Acceptor, see next option) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]da</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-r2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Second cutoff radius. Mainly useful with -contact and -ac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]da</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-r2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Second cutoff radius. Mainly useful with <tt>-contact</tt> and <tt>-ac</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-abin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Binwidth angle distribution (degrees) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.005 </tt> </TD><TD> Binwidth distance distribution (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nitacc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Regard nitrogen atoms as acceptors </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]contact</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do not look for hydrogen bonds, but merely for contacts within the cut-off distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nitacc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Regard nitrogen atoms as acceptors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]contact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do not look for hydrogen bonds, but merely for contacts within the cut-off distance </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> when > 0, only calculate hydrogen bonds within # nm shell around one particle </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. With -gemfit we suggest -fitstart 0 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with -gemfit) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. With <tt>-gemfit</tt> we suggest <tt>-fitstart 0</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with <tt>-gemfit</tt>) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-smooth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dump</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Dump the first N hydrogen bond ACFs in a single <a href="xvg.html">xvg</a> file for debugging </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-smooth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/τ) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dump</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Dump the first N hydrogen bond ACFs in a single <tt>.<a href="xvg.html">xvg</a></tt> file for debugging </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-max_hb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]merge</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]merge</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-geminate</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Use reversible geminate recombination for the kinetics/thermodynamics calclations. See Markovitch et al., J. Chem. Phys 129, 084505 (2008) for details.: <tt>none</tt>, <tt>dd</tt>, <tt>ad</tt>, <tt>aa</tt> or <tt>a4</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-diff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Dffusion coefficient to use in the rev. gem. recomb. kinetic model. If non-positive, then it will be fitted to the ACF along with ka and kd. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-diff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Dffusion coefficient to use in the reversible geminate recombination kinetic model. If negative, then it will be fitted to the ACF along with ka and kd. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nthreads</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of threads used for the parallel loop over autocorrelations. nThreads <= 0 means maximum number of threads. Requires linking with OpenMP. The number of threads is limited by the number of processors (before OpenMP v.3 ) or environment variable OMP_THREAD_LIMIT (OpenMP v.3) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_helix</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_helix computes all kind of helix properties. First, the peptide
-is checked to find the longest helical part. This is determined by
-Hydrogen bonds and Phi/Psi angles.
+<tt>g_helix</tt> computes all kinds of helix properties. First, the peptide
+is checked to find the longest helical part, as determined by
+hydrogen bonds and φ/ψ angles.
That bit is fitted
-to an ideal helix around the Z-axis and centered around the origin.
+to an ideal helix around the <it>z</it>-axis and centered around the origin.
Then the following properties are computed:<p>
-<b>1.</b> Helix radius (file radius.<a href="xvg.html">xvg</a>). This is merely the
-RMS deviation in two dimensions for all Calpha atoms.
-it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number
+<b>1.</b> Helix radius (file <tt>radius.<a href="xvg.html">xvg</a></tt>). This is merely the
+RMS deviation in two dimensions for all Cα atoms.
+it is calculated as sqrt((sum_i (x^2(i)+y^2(i)))/N) where N is the number
of backbone atoms. For an ideal helix the radius is 0.23 nm<br>
-<b>2.</b> Twist (file twist.<a href="xvg.html">xvg</a>). The average helical angle per
-residue is calculated. For alpha helix it is 100 degrees,
-for 3-10 helices it will be smaller,
+<b>2.</b> Twist (file <tt>twist.<a href="xvg.html">xvg</a></tt>). The average helical angle per
+residue is calculated. For an α-helix it is 100 degrees,
+for 3-10 helices it will be smaller, and
for 5-helices it will be larger.<br>
-<b>3.</b> Rise per residue (file rise.<a href="xvg.html">xvg</a>). The helical rise per
-residue is plotted as the difference in Z-coordinate between Ca
-atoms. For an ideal helix this is 0.15 nm<br>
-<b>4.</b> Total helix length (file len-ahx.<a href="xvg.html">xvg</a>). The total length
+<b>3.</b> Rise per residue (file <tt>rise.<a href="xvg.html">xvg</a></tt>). The helical rise per
+residue is plotted as the difference in <it>z</it>-coordinate between Cα
+atoms. For an ideal helix, this is 0.15 nm<br>
+<b>4.</b> Total helix length (file <tt>len-ahx.<a href="xvg.html">xvg</a></tt>). The total length
of the
helix in nm. This is simply the average rise (see above) times the
number of helical residues (see below).<br>
-<b>5.</b> Number of helical residues (file n-ahx.<a href="xvg.html">xvg</a>). The title says
-it all.<br>
-<b>6.</b> Helix Dipole, backbone only (file dip-ahx.<a href="xvg.html">xvg</a>).<br>
-<b>7.</b> RMS deviation from ideal helix, calculated for the Calpha
-atoms only (file rms-ahx.<a href="xvg.html">xvg</a>).<br>
-<b>8.</b> Average Calpha-Calpha dihedral angle (file phi-ahx.<a href="xvg.html">xvg</a>).<br>
-<b>9.</b> Average Phi and Psi angles (file phipsi.<a href="xvg.html">xvg</a>).<br>
-<b>10.</b> Ellipticity at 222 nm according to <it>Hirst and Brooks</it>
+<b>5.</b> Helix dipole, backbone only (file <tt>dip-ahx.<a href="xvg.html">xvg</a></tt>).<br>
+<b>6.</b> RMS deviation from ideal helix, calculated for the Cα
+atoms only (file <tt>rms-ahx.<a href="xvg.html">xvg</a></tt>).<br>
+<b>7.</b> Average Cα - Cα dihedral angle (file <tt>phi-ahx.<a href="xvg.html">xvg</a></tt>).<br>
+<b>8.</b> Average φ and ψ angles (file <tt>phipsi.<a href="xvg.html">xvg</a></tt>).<br>
+<b>9.</b> Ellipticity at 222 nm according to Hirst and Brooks.
<p>
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The first residue number in the sequence </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Check at every step which part of the sequence is helical </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]F</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Toggle fit to a perfect helix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]db</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print debug info </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Check at every step which part of the sequence is helical </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]F</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Toggle fit to a perfect helix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]db</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print debug info </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-prop</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>RAD</tt> </TD><TD> Select property to weight eigenvectors with. WARNING experimental stuff: <tt>RAD</tt>, <tt>TWIST</tt>, <tt>RISE</tt>, <tt>LEN</tt>, <tt>NHX</tt>, <tt>DIP</tt>, <tt>RMS</tt>, <tt>CPHI</tt>, <tt>RMSA</tt>, <tt>PHI</tt>, <tt>PSI</tt>, <tt>HB3</tt>, <tt>HB4</tt>, <tt>HB5</tt> or <tt>CD222</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ev</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write a new 'trajectory' file for ED </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ev</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write a new 'trajectory' file for ED </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ahxstart</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> First residue in helix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ahxend</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Last residue in helix </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_helixorient</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_helixorient calculates the coordinates and direction of the average
+<tt>g_helixorient</tt> calculates the coordinates and direction of the average
axis inside an alpha helix, and the direction/vectors of both the
-
alpha carbon and (optionally) a sidechain atom relative to the axis.<p>
-As input, you need to specify an index group with alpha carbon atoms
-corresponding to an alpha helix of continuous residues. Sidechain
+
Cα and (optionally) a sidechain atom relative to the axis.<p>
+As input, you need to specify an index group with Cα atoms
+corresponding to an α-helix of continuous residues. Sidechain
directions require a second index group of the same size, containing
the heavy atom in each residue that should represent the sidechain.<p>
-
Note that this program does not do any fitting of structures.<p>
-We need four Calpha coordinates to define the local direction of the helix
+
<b>Note</b> that this program does not do any fitting of structures.<p>
+We need four Cα coordinates to define the local direction of the helix
axis.<p>
The tilt/rotation is calculated from Euler rotations, where we define
-the helix axis as the local X axis, the residues/CA-vector as Y, and the
-Z axis from their cross product. We use the Euler Y-Z-X rotation, meaning
+the helix axis as the local <it>x</it>-axis, the residues/Cα vector as <it>y</it>, and the
+<it>z</it>-axis from their cross product. We use the Euler Y-Z-X rotation, meaning
we first tilt the helix axis (1) around and (2) orthogonal to the residues
vector, and finally apply the (3) rotation around it. For debugging or other
-purposes, we also write out the actual Euler rotation angles as theta1-3.<a href="xvg.html">xvg</a>
+purposes, we also write out the actual Euler rotation angles as <tt>theta[1-3].<a href="xvg.html">xvg</a></tt>
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sidechain</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate sidechain directions relative to helix axis too. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]incremental</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate incremental rather than total rotation/tilt. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sidechain</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate sidechain directions relative to helix axis too. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]incremental</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate incremental rather than total rotation/tilt. </TD></TD>
</TABLE>
<P>
<hr>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>g_hydorder</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
+<TABLE WIDTH="98%" NOBORDER >
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
+<TD WIDTH=116>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_hydorder</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
+<HR>
+<H3>Description</H3>
+<p>
+g_hydorder computes the tetrahedrality order parameters around a
+given atom. Both angle an distance order parameters are calculated. See
+P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.
+for more details.<br>This application calculates the orderparameter in a 3d-mesh in the box, and
+with 2 phases in the box gives the user the option to define a 2D interface in time
+separating the faces by specifying parameters -sgang1 and -sgang2 (It is important
+to select these judiciously)
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> intf.xpm</a></tt> </TD><TD> Output, Mult. </TD><TD> X PixMap compatible matrix file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html"> raw.out</a></tt> </TD><TD> Output, Opt., Mult. </TD><TD> Generic output file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-Spect</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html">intfspect.out</a></tt> </TD><TD> Output, Opt., Mult. </TD><TD> Generic output file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> Direction of the normal on the membrane: <tt>z</tt>, <tt>x</tt> or <tt>y</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Binwidth of box mesh </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sgang1</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> tetrahedral angle parameter in Phase 1 (bulk) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sgang2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> tetrahedral angle parameter in Phase 2 (bulk) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tblock</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of frames in one time-block average </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevel</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Number of Height levels in 2D - XPixMaps </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>g_kinetics</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
+<TABLE WIDTH="98%" NOBORDER >
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
+<TD WIDTH=116>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_kinetics</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
+<HR>
+<H3>Description</H3>
+<p>
+<tt>g_kinetics</tt> reads two <tt>.<a href="xvg.html">xvg</a></tt> files, each one containing data for N replicas.
+The first file contains the temperature of each replica at each timestep,
+and the second contains real values that can be interpreted as
+an indicator for folding. If the value in the file is larger than
+the cutoff it is taken to be unfolded and the other way around.<p>
+From these data an estimate of the forward and backward rate constants
+for folding is made at a reference temperature. In addition,
+a theoretical melting curve and free energy as a function of temperature
+are printed in an <tt>.<a href="xvg.html">xvg</a></tt> file.<p>
+The user can give a max value to be regarded as intermediate
+(<tt>-ucut</tt>), which, when given will trigger the use of an intermediate state
+in the algorithm to be defined as those structures that have
+cutoff < DATA < ucut. Structures with DATA values larger than ucut will
+not be regarded as potential folders. In this case 8 parameters are optimized.<p>
+The average fraction foled is printed in an <tt>.<a href="xvg.html">xvg</a></tt> file together with the fit to it.
+If an intermediate is used a further file will show the build of the intermediate and the fit to that process.<p>
+The program can also be used with continuous variables (by setting
+<tt>-nodiscrete</tt>). In this case kinetics of other processes can be
+studied. This is very much a work in progress and hence the manual
+(this information) is lagging behind somewhat.<p>
+In order to compile this program you need access to the GNU
+scientific library.
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> temp.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> data.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-d2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> data2.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> ft_all.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> it_all.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o3</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> ft_repl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ee</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> err_est.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> remd.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-m</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> melt.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Expect a time in the input </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First time to read from set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last time to read from set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time to start the fit from </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-efit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time to end the fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Reference temperature for computing rate constants </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read data for this number of replicas. Only necessary when files are written in xmgrace format using @type and & as delimiters. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.2 </tt> </TD><TD> Cut-off (max) value for regarding a structure as folded </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ucut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Cut-off (max) value for regarding a structure as intermediate (if not folded) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-euf</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>10 </tt> </TD><TD> Initial guess for energy of activation for folding (kJ/mol) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-efu</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>30 </tt> </TD><TD> Initial guess for energy of activation for unfolding (kJ/mol) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>10 </tt> </TD><TD> Initial guess for energy of activation for intermediates (kJ/mol) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxiter</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Max number of iterations </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]back</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Take the back reaction into account </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Absolute tolerance for convergence of the Nelder and Mead simplex algorithm </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip points in the output <tt>.<a href="xvg.html">xvg</a></tt> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Estimate error by splitting the number of replicas in two and refitting </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average folding before computing χ^2 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]discrete</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use a discrete folding criterion (F <-> U) or a continuous one </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mult</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Factor to multiply the data with before discretization </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_lie</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_lie computes a free energy estimate based on an energy analysis
+<tt>g_lie</tt> computes a free energy estimate based on an energy analysis
from. One needs an energy file with the following components:
Coul (A-B) LJ-SR (A-B) etc.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-Elj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Lennard-Jones interaction between ligand and solvent </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-Eqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Coulomb interaction between ligand and solvent </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mdmat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_mdmat makes distance matrices consisting of the smallest distance
-between residue pairs. With -frames these distance matrices can be
-stored as a function
-of time, to be able to see differences in tertiary structure as a
-funcion of time. If you choose your options unwise, this may generate
-a large output file. Default only an averaged matrix over the whole
+<tt>g_mdmat</tt> makes distance matrices consisting of the smallest distance
+between residue pairs. With <tt>-frames</tt>, these distance matrices can be
+stored in order to see differences in tertiary structure as a
+function of time. If you choose your options unwisely, this may generate
+a large output file. By default, only an averaged matrix over the whole
trajectory is output.
Also a count of the number of different atomic contacts between
residues over the whole trajectory can be made.
-The output can be processed with <a href="xpm2ps.html">xpm2ps</a> to make a PostScript (tm) plot.
+The output can be processed with <tt><a href="xpm2ps.html">xpm2ps</a></tt> to make a PostScript (tm) plot.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1.5 </tt> </TD><TD> trunc distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize distance in # levels </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize distance in this number of levels </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_membed</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_membed embeds a membrane protein into an equilibrated lipid bilayer at the position
-and orientation specified by the user.
-
-
-
-SHORT MANUAL
-------------
-
+<tt>g_membed</tt> embeds a membrane protein into an equilibrated lipid bilayer at the position
+and orientation specified by the user.<p>
+SHORT MANUAL<br>------------<br>
The user should merge the structure files of the protein and membrane (+solvent), creating a
single structure file with the protein overlapping the membrane at the desired position and
-orientation. Box size should be taken from the membrane structure file. The corresponding topology
-files should also be merged. Consecutively, create a <a href="tpr.html">tpr</a> file (input for g_membed) from these files,with the following options included in the <a href="mdp.html">mdp</a> file.
-
- - integrator = md
-
- - energygrp = Protein (or other group that you want to insert)
-
- - freezegrps = Protein
-
- - freezedim = Y Y Y
-
- - energygrp_excl = Protein Protein
-
+orientation. The box size is taken from the membrane structure file. The corresponding topology
+files should also be merged. Consecutively, create a <tt>.<a href="tpr.html">tpr</a></tt> file (input for <tt>g_membed</tt>) from these files,with the following options included in the <tt>.<a href="mdp.html">mdp</a></tt> file.<br>
+ - <tt>integrator = md</tt><br>
+ - <tt>energygrp = Protein</tt> (or other group that you want to insert)<br>
+ - <tt>freezegrps = Protein</tt><br>
+ - <tt>freezedim = Y Y Y</tt><br>
+ - <tt>energygrp_excl = Protein Protein</tt><br>
The output is a structure file containing the protein embedded in the membrane. If a topology
file is provided, the number of lipid and
-solvent molecules will be updated to match the new structure file.
-
-For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.
-
-
-
-SHORT METHOD DESCRIPTION
-
-------------------------
-
-1. The protein is resized around its center of mass by a factor -xy in the xy-plane
-(the membrane plane) and a factor -z in the z-direction (if the size of the
+solvent molecules will be updated to match the new structure file.<br>
+For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.<p>
+SHORT METHOD DESCRIPTION<br>
+------------------------<br>
+1. The protein is resized around its center of mass by a factor <tt>-xy</tt> in the xy-plane
+(the membrane plane) and a factor <tt>-z</tt> in the <it>z</it>-direction (if the size of the
protein in the z-direction is the same or smaller than the width of the membrane, a
--z value larger than 1 can prevent that the protein will be enveloped by the lipids).
-
+<tt>-z</tt> value larger than 1 can prevent that the protein will be enveloped by the lipids).<br>
2. All lipid and solvent molecules overlapping with the resized protein are removed. All
-intraprotein interactions are turned off to prevent numerical issues for small values of -xy
- or -z
-
-3. One md step is performed.
-
-4. The resize factor (-xy or -z) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the
+intraprotein interactions are turned off to prevent numerical issues for small values of <tt>-xy</tt>
+ or <tt>-z</tt><br>
+3. One md step is performed.<br>
+4. The resize factor (<tt>-xy</tt> or <tt>-z</tt>) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the
protein is resized again around its center of mass. The resize factor for the xy-plane
-is incremented first. The resize factor for the z-direction is not changed until the -xy factor
-is 1 (thus after -nxy iteration).
-
-5. Repeat step 3 and 4 until the protein reaches its original size (-nxy + -nz iterations).
-
-For a more extensive method descrition see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.
-
-
-
-NOTE
-----
-
- - Protein can be any molecule you want to insert in the membrane.
-
+is incremented first. The resize factor for the z-direction is not changed until the <tt>-xy</tt> factor
+is 1 (thus after <tt>-nxy</tt> iterations).<br>
+5. Repeat step 3 and 4 until the protein reaches its original size (<tt>-nxy</tt> + <tt>-nz</tt> iterations).<br>
+For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.<p>
+NOTE<br>----<br>
+ - Protein can be any molecule you want to insert in the membrane.<br>
- It is recommended to perform a short equilibration run after the embedding
-(see Wolf et al, J Comp Chem 31 (2010) 2169-2174, to re-equilibrate the membrane. Clearly
-protein equilibration might require longer.
-
-
-
+(see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly
+protein equilibration might require longer.<p>
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> topol.top</a></tt> </TD><TD> In/Out, Opt. </TD><TD> Topology file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-x</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xtc.html"> traj.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Compressed trajectory (portable xdr format) </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-cpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html"> state.cpt</a></tt> </TD><TD> Input, Opt. </TD><TD> Checkpoint file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-cpo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html"> state.cpt</a></tt> </TD><TD> Output, Opt. </TD><TD> Checkpoint file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">membedded.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html"> ener.edr</a></tt> </TD><TD> Output </TD><TD> Energy file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> md.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html"> sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-tablep</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tablep.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-tableb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-dhdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-field</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> field.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-tablep</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tablep.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-tableb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-tpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpi.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-tpid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpidist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html"> sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html"> sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-j</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html"> wham.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-jo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html"> bam.gct</a></tt> </TD><TD> Output, Opt. </TD><TD> General coupling stuff </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> gct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-devout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">deviatie.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-runav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> runaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-px</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pullx.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-pf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pullf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-mtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> nm.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> dipole.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-dat</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> membed.dat</a></tt> </TD><TD> Output </TD><TD> Generic data file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-deffnm</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Set the default filename for all file options </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xyinit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> Resize factor for the protein in the xy dimension before starting embedding </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xyend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Final resize factor in the xy dimension </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-zinit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Resize factor for the protein in the z dimension before starting embedding </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nz</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of iterations for the z dimension </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rad</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.22 </tt> </TD><TD> Probe radius to check for overlap between the group to embed and the membrane </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-pieces</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own geometrical center. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]asymmetry</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]asymmetry</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ndiff</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of lipids that will additionally be removed from the lower (negative number) or upper (positive number) membrane leaflet. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-maxwarn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Maximum number of warning allowed </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Write a compact <a href="log.html">log</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]start</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Call <a href="mdrun.html">mdrun</a> with membed options </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mdrun_path</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Path to the <a href="mdrun.html">mdrun</a> executable compiled with this g_membed version </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mindist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_mindist computes the distance between one group and a number of
+<tt>g_mindist</tt> computes the distance between one group and a number of
other groups. Both the minimum distance
(between any pair of atoms from the respective groups)
and the number of contacts within a given
distance are written to two separate output files.
-With the <tt>-group</tt> option a contact of an atom an other group
+With the <tt>-group</tt> option a contact of an atom in another group
with multiple atoms in the first group is counted as one contact
instead of as multiple contacts.
With <tt>-or</tt>, minimum distances to each residue in the first
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]matrix</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate half a matrix of group-group distances </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]max</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate *maximum* distance instead of minimum </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]matrix</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate half a matrix of group-group distances </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]max</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate *maximum* distance instead of minimum </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.6 </tt> </TD><TD> Distance for contacts </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]group</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Count contacts with multiple atoms in the first group as one </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pi</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate minimum distance with periodic images </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split graph where time is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]group</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Count contacts with multiple atoms in the first group as one </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate minimum distance with periodic images </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split graph where time is zero </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of secondary groups to compute distance to a central group </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Take periodic boundary conditions into account </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]respertime</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> When writing per-residue distances, write distance for each time point </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]printresname</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write residue names </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Take periodic boundary conditions into account </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]respertime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> When writing per-residue distances, write distance for each time point </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]printresname</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write residue names </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_morph</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_morph does a linear interpolation of conformations in order to
+<tt>g_morph</tt> does a linear interpolation of conformations in order to
create intermediates. Of course these are completely unphysical, but
that you may try to justify yourself. Output is in the form of a
generic trajectory. The number of intermediates can be controlled with
-the -ninterm flag. The first and last flag correspond to the way of
+the <tt>-ninterm</tt> flag. The first and last flag correspond to the way of
interpolating: 0 corresponds to input structure 1 while
1 corresponds to input structure 2.
-If you specify first < 0 or last > 1 extrapolation will be
-on the path from input structure x1 to x2. In general the coordinates
-of the intermediate x(i) out of N total interm
idates correspond to:<p>
-x(i) = x
1 + (first+(i/(N-1))*(last-first))*(x2-x1)<p>
+If you specify <tt>-first</tt> < 0 or <tt>-last</tt> > 1 extrapolation will be
+on the path from input structure x_1 to x_2. In general, the coordinates
+of the intermediate x(i) out of N total interm
ediates correspond to:<p>
+x(i) = x
_1 + (first+(i/(N-1))*(last-first))*(x_2-x_1)<p>
Finally the RMSD with respect to both input structures can be computed
-if explicitly selected (-or option). In that case an index file may be
-read to select what group RMS is computed from.
+if explicitly selected (<tt>-or</tt> option). In that case, an index file may be
+read to select the group from which the RMS is computed.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ninterm</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>11</tt> </TD><TD> Number of intermediates </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Corresponds to first generated structure (0 is input x0, see above) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Corresponds to last generated structure (1 is input x1, see above) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do a least squares fit of the second to the first structure before interpolating </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Corresponds to first generated structure (0 is input x_1, see above) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Corresponds to last generated structure (1 is input x_2, see above) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do a least squares fit of the second to the first structure before interpolating </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_msd</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_msd computes the mean square displacement (MSD) of atoms from
+<tt>g_msd</tt> computes the mean square displacement (MSD) of atoms from
a set of initial positions. This provides an easy way to compute
the diffusion constant using the Einstein relation.
The time between the reference points for the MSD calculation
types of mean square displacement: <tt>-type</tt>, <tt>-lateral</tt>
and <tt>-ten</tt>. Option <tt>-ten</tt> writes the full MSD tensor for
each group, the order in the output is: trace xx yy zz yx zx zy.<p>
-If <tt>-mol</tt> is set, g_msd plots the MSD for individual molecules:
+If <tt>-mol</tt> is set, <tt>g_msd</tt> plots the MSD for individual molecules
+(including making molecules whole across periodic boundaries):
for each individual molecule a diffusion constant is computed for
its center of mass. The chosen index group will be split into
molecules.<p>
With the option <tt>-rmcomm</tt>, the center of mass motion of a
specific group can be removed. For trajectories produced with
GROMACS this is usually not necessary,
-as <a href="mdrun.html">mdrun</a> usually already removes the center of mass motion.
+as <tt><a href="mdrun.html">mdrun</a></tt> usually already removes the center of mass motion.
When you use this option be sure that the whole system is stored
in the trajectory file.<p>
The diffusion coefficient is determined by linear regression of the MSD,
Note that this diffusion coefficient and error estimate are only
accurate when the MSD is completely linear between
<tt>-beginfit</tt> and <tt>-endfit</tt>.<p>
-Option <tt>-<a href="pdb.html">pdb</a></tt> writes a <a href="pdb.html">pdb</a> file with the coordinates of the frame
+Option <tt>-<a href="pdb.html">pdb</a></tt> writes a <tt>.<a href="pdb.html">pdb</a></tt> file with the coordinates of the frame
at time <tt>-tpdb</tt> with in the B-factor field the square root of
the diffusion coefficient of the molecule.
This option implies option <tt>-mol</tt>.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Compute diffusion coefficient in one direction: <tt>no</tt>, <tt>x</tt>, <tt>y</tt> or <tt>z</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-lateral</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Calculate the lateral diffusion in a plane perpendicular to: <tt>no</tt>, <tt>x</tt>, <tt>y</tt> or <tt>z</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ten</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the full tensor </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ten</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the full tensor </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ngroup</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to calculate MSD for </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Mass weighted MSD </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmcomm</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove center of mass motion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tpdb</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> The frame to use for option -<a href="pdb.html">pdb</a> (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Mass weighted MSD </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmcomm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove center of mass motion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tpdb</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> The frame to use for option <tt>-<a href="pdb.html">pdb</a></tt> (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-trestart</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>10 </tt> </TD><TD> Time between restarting points in trajectory (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Start time for fitting the MSD (ps), -1 is 10% </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> End time for fitting the MSD (ps), -1 is 90% </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,
+<tt>g_nmeig</tt> calculates the eigenvectors/values of a (Hessian) matrix,
which can be calculated with <tt><a href="mdrun.html">mdrun</a></tt>.
The eigenvectors are written to a trajectory file (<tt>-v</tt>).
The structure is written first with t=0. The eigenvectors
The eigenvectors can be analyzed with <tt><a href="g_anaeig.html">g_anaeig</a></tt>.
An ensemble of structures can be generated from the eigenvectors with
<tt><a href="g_nmens.html">g_nmens</a></tt>. When mass weighting is used, the generated eigenvectors
-will be scaled back to plain cartesian coordinates before generating the
-output - in this case they will no longer be exactly orthogonal in the
-standard cartesian norm (But in the mass weighted norm they would be).
+will be scaled back to plain Cartesian coordinates before generating the
+output. In this case, they will no longer be exactly orthogonal in the
+standard Cartesian norm, but in the mass-weighted norm they would be.<p>
+This program can be optionally used to compute quantum corrections to heat capacity
+and enthalpy by providing an extra file argument <tt>-qcorr</tt>. See the GROMACS
+manual, Chapter 1, for details. The result includes subtracting a harmonic
+degree of freedom at the given temperature.
+The total correction is printed on the terminal screen.
+The recommended way of getting the corrections out is:<p>
+<tt>g_nmeig -s topol.<a href="tpr.html">tpr</a> -f nm.<a href="mtx.html">mtx</a> -first 7 -last 10000 -T 300 -qc [-constr]</tt><p>
+The <tt>-constr</tt> option should be used when bond constraints were used during the
+simulation <b>for all the covalent bonds</b>. If this is not the case,
+you need to analyze the <tt>quant_corr.<a href="xvg.html">xvg</a></tt> file yourself.<p>
+To make things more flexible, the program can also take virtual sites into account
+when computing quantum corrections. When selecting <tt>-constr</tt> and
+<tt>-qc</tt>, the <tt>-begin</tt> and <tt>-end</tt> options will be set automatically as well.
+Again, if you think you know it better, please check the <tt>eigenfreq.<a href="xvg.html">xvg</a></tt>
+output.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> hessian.mtx</a></tt> </TD><TD> Input </TD><TD> Hessian matrix </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenfreq.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-os</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">spectrum.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-qc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">quant_corr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> First eigenvector to write away </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>50</tt> </TD><TD> Last eigenvector to write away </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxspec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>4000</tt> </TD><TD> Highest frequency (1/cm) to consider in the spectrum </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for computing quantum heat capacity and enthalpy when using normal mode calculations to correct classical simulations </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]constr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> If constraints were used in the simulation but not in the normal mode analysis (this is the recommended way of doing it) you will need to set this for computing the quantum corrections. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-width</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Width (sigma) of the gaussian peaks (1/cm) when generating a spectrum </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmens</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<tt>g_nmens</tt> generates an ensemble around an average structure
-in a subspace which is defined by a set of normal modes (eigenvectors).
+in a subspace that is defined by a set of normal modes (eigenvectors).
The eigenvectors are assumed to be mass-weighted.
The position along each eigenvector is randomly taken from a Gaussian
distribution with variance kT/eigenvalue.<p>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Temperature in Kelvin </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmtraj</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<tt>g_nmtraj</tt> generates an virtual trajectory from an eigenvector,
-corresponding to a harmonic cartesian oscillation around the average
+corresponding to a harmonic Cartesian oscillation around the average
structure. The eigenvectors should normally be mass-weighted, but you can
use non-weighted eigenvectors to generate orthogonal motions.
The output frames are written as a trajectory file covering an entire period, and
PDB format you can view it directly in PyMol and also render a photorealistic movie.
Motion amplitudes are calculated from the eigenvalues and a preset temperature,
assuming equipartition of the energy over all modes. To make the motion clearly visible
-in PyMol you might want to amplify it by setting an unrealistic high temperature.
-However, be aware that both the linear cartesian displacements and mass weighting will
+in PyMol you might want to amplify it by setting an unrealistically high temperature.
+However, be aware that both the linear Cartesian displacements and mass weighting will
lead to serious structure deformation for high amplitudes - this is is simply a limitation
-of the cartesian normal mode model. By default the selected eigenvector is set to 7, since
+of the Cartesian normal mode model. By default the selected eigenvector is set to 7, since
the first six normal modes are the translational and rotational degrees of freedom.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-eignr</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>7</tt> </TD><TD> String of eigenvectors to use (first is 1) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-phases</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>0.0</tt> </TD><TD> String of phases (default is 0.0) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Temperature in Kelvin </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Temperature (K) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-amplitude</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.25 </tt> </TD><TD> Amplitude for modes with eigenvalue<=0 </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nframes</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>30</tt> </TD><TD> Number of frames to generate </TD></TD>
</TABLE>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>g_options</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
+<TABLE WIDTH="98%" NOBORDER >
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
+<TD WIDTH=116>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_options</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
+<HR>
+<H3>Description</H3>
+<p>
+GROMACS programs have some standard options,
+of which some are hidden by default:
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+</TABLE>
+<P>
+<H3>Known problems</H3>
+<UL>
+<LI>If the configuration script found Motif or Lesstif on your system, you can use the graphical interface (if not, you will get an error):<br><tt>-X</tt> gmx_bool <tt>no</tt> Use dialog box GUI to edit command line options
+<LI>When compiled on an SGI-IRIX system, all GROMACS programs have an additional option:<br><tt>-npri</tt> int <tt>0</tt> Set non blocking priority (try 128)
+<LI>Optional files are not used unless the option is set, in contrast to non-optional files, where the default file name is used when the option is not set.
+<LI>All GROMACS programs will accept file options without a file extension or filename being specified. In such cases the default filenames will be used. With multiple input file types, such as generic structure format, the directory will be searched for files of each type with the supplied or default name. When no such file is found, or with output files the first file type will be used.
+<LI>All GROMACS programs with the exception of <tt><a href="mdrun.html">mdrun</a></tt> and <tt><a href="eneconv.html">eneconv</a></tt> check if the command line options are valid. If this is not the case, the program will be halted.
+<LI>Enumerated options (enum) should be used with one of the arguments listed in the option description, the argument may be abbreviated. The first match to the shortest argument in the list will be selected.
+<LI>Vector options can be used with 1 or 3 parameters. When only one parameter is supplied the two others are also set to this value.
+<LI>All GROMACS programs can read compressed or g-zipped files. There might be a problem with reading compressed <tt>.<a href="xtc.html">xtc</a></tt>, <tt>.<a href="trr.html">trr</a></tt> and <tt>.<a href="trj.html">trj</a></tt> files, but these will not compress very well anyway.
+<LI>Most GROMACS programs can process a trajectory with fewer atoms than the run input or structure file, but only if the trajectory consists of the first n atoms of the run input or structure file.
+<LI>Many GROMACS programs will accept the <tt>-tu</tt> option to set the time units to use in output files (e.g. for <tt>xmgr</tt> graphs or <tt><a href="xpm.html">xpm</a></tt> matrices) and in all time options.
+</UL>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
parameters however, which only work for water anyway).<p>
The program can also give all
diagonal elements of the order tensor and even calculate the deuterium
-order parameter Scd (default). If the option -szonly is given, only one
-order tensor component (specified by the -d option) is given and the
-order parameter per slice is calculated as well. If -szonly is not
+order parameter Scd (default). If the option <tt>-szonly</tt> is given, only one
+order tensor component (specified by the <tt>-d</tt> option) is given and the
+order parameter per slice is calculated as well. If <tt>-szonly</tt> is not
selected, all diagonal elements and the deuterium order parameter is
given.<p>The tetrahedrality order parameters can be determined
around an atom. Both angle an distance order parameters are calculated. See
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> Direction of the normal on the membrane: <tt>z</tt>, <tt>x</tt> or <tt>y</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Calculate order parameter as function of boxlength, dividing the box in #nr slices. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]szonly</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only give Sz element of order tensor. (axis can be specified with -d) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]unsat</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]permolecule</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute per-molecule Scd order parameters </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]radial</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute a radial membrane normal </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]calcdist</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute distance from a reference (currently defined only for radial and permolecule) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Calculate order parameter as function of box length, dividing the box into this number of slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]szonly</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only give Sz element of order tensor. (axis can be specified with <tt>-d</tt>) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]unsat</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]permolecule</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute per-molecule Scd order parameters </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]radial</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute a radial membrane normal </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]calcdist</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute distance from a reference (currently defined only for radial and permolecule) </TD></TD>
</TABLE>
<P>
<hr>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>g_pme_error</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
+<TABLE WIDTH="98%" NOBORDER >
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
+<TD WIDTH=116>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_pme_error</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
+<HR>
+<H3>Description</H3>
+<p>
+<tt>g_pme_error</tt> estimates the error of the electrostatic forces
+if using the sPME algorithm. The flag <tt>-tune</tt> will determine
+the splitting parameter such that the error is equally
+distributed over the real and reciprocal space part.
+The part of the error that stems from self interaction of the particles is computationally demanding. However, a good a approximation is to
+just use a fraction of the particles for this term which can be
+indicated by the flag <tt>-self</tt>.<p>
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html"> error.out</a></tt> </TD><TD> Output </TD><TD> Generic output file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-so</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> tuned.tpr</a></tt> </TD><TD> Output, Opt. </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beta</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> If positive, overwrite ewald_beta from <tt>.<a href="tpr.html">tpr</a></tt> file with this value </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]tune</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Tune the splitting parameter such that the error is equally distributed between real and reciprocal space </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-self</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> If between 0.0 and 1.0, determine self interaction error from just this fraction of the charged particles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Random number seed used for Monte Carlo algorithm when <tt>-self</tt> is set to a value between 0.0 and 1.0 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_polystat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_polystat plots static properties of polymers as a function of time
+<tt>g_polystat</tt> plots static properties of polymers as a function of time
and prints the average.<p>
By default it determines the average end-to-end distance and radii
of gyration of polymers. It asks for an index group and split this
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use the mass weighting for radii of gyration </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot average eigenvalues </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use the mass weighting for radii of gyration </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot average eigenvalues </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_potential</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-Compute the electrostatical potential across the box. The potential is
+<tt>g_potential</tt> computes the electrostatical potential across the box. The potential is
calculated by first summing the charges per slice and then integrating
twice of this charge distribution. Periodic boundaries are not taken
into account. Reference of potential is taken to be the left side of
-the box. It's also possible to calculate the potential in spherical
+the box. It is also possible to calculate the potential in spherical
coordinates as function of r by calculating a charge distribution in
spherical slices and twice integrating them. epsilon_r is taken as 1,
-2 is more appropriate in many cases.
+but 2 is more appropriate in many cases.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Calculate potential as function of boxlength, dividing the box in #nr slices. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-cb</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Discard first #nr slices of box for integration </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ce</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Discard last #nr slices of box for integration </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tz</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Translate all coordinates <distance> in the direction of the box </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]spherical</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate spherical thingie </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Calculate potential as function of boxlength, dividing the box in this number of slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cb</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Discard this number of first slices of box for integration </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ce</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Discard this number of last slices of box for integration </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tz</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Translate all coordinates by this distance in the direction of the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]spherical</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate spherical thingie </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to consider </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]correct</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Assume net zero charge of groups to improve accuracy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]correct</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Assume net zero charge of groups to improve accuracy </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_principal</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_principal calculates the three principal axes of inertia for a group
+<tt>g_principal</tt> calculates the three principal axes of inertia for a group
of atoms.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]foo</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Dummy option to avoid empty array </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]foo</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Dummy option to avoid empty array </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_protonate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-<tt><a href="protonate.html">protonate</a></tt> reads (a) conformation(s) and adds all missing
-hydrogens as defined in <tt>
ffgmx2.<a href="hdb.html">hdb</a></tt>. If only <tt>-s</tt> is
+<tt>
g_<a href="protonate.html">protonate</a></tt> reads (a) conformation(s) and adds all missing
+hydrogens as defined in <tt>
gmx2.ff/aminoacids.<a href="hdb.html">hdb</a></tt>. If only <tt>-s</tt> is
specified, this conformation will be protonated, if also <tt>-f</tt>
-is specified, the conformation(s) will be read from this file
+is specified, the conformation(s) will be read from this file,
which can be either a single conformation or a trajectory.
<p>
-If a <a href="pdb.html">pdb</a> file is supplied, residue names might not correspond to
+If a <tt>.<a href="pdb.html">pdb</a></tt> file is supplied, residue names might not correspond to
to the GROMACS naming conventions, in which case these residues will
probably not be properly protonated.
<p>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
+<UL>
+<LI>For the moment, only .<a href="pdb.html">pdb</a> files are accepted to the -s flag
+</UL>
+<P>
<hr>
<div ALIGN=RIGHT>
<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_rama selects the Phi/Psi dihedral combinations from your topology file
+<tt>g_rama</tt> selects the φ/ψ dihedral combinations from your topology file
and computes these as a function of time.
Using simple Unix tools such as <it>grep</it> you can select out
specific residues.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
</TABLE>
<P>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rdf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
scattering. The most common way to describe liquid structure is by a
radial distribution function. However, this is not easy to obtain from
a scattering experiment.<p>
-g_rdf calculates radial distribution functions in different ways.
+<tt>g_rdf</tt> calculates radial distribution functions in different ways.
The normal method is around a (set of) particle(s), the other methods
are around the center of mass of a set of particles (<tt>-com</tt>)
or to the closest particle in a set (<tt>-surf</tt>).
-With all methods rdf's can also be calculated around axes parallel
-to the z-axis with option <tt>-xy</tt>.
+With all methods, the RDF can also be calculated around axes parallel
+to the <it>z</it>-axis with option <tt>-xy</tt>.
With option <tt>-surf</tt> normalization can not be used.<p>
-The option <tt>-rdf</tt> sets the type of rdf to be computed.
+The option <tt>-rdf</tt> sets the type of RDF to be computed.
Default is for atoms or particles, but one can also select center
-of mass or geometry of molecules or residues. In all cases only
+of mass or geometry of molecules or residues. In all cases, only
the atoms in the index groups are taken into account.
-For molecules and/or the center of mass option a run input file
+For molecules and/or the center of mass option, a run input file
is required.
-Other weighting than COM or COG can currently only be achieved
+Weighting other than COM or COG can currently only be achieved
by providing a run input file with different masses.
Options <tt>-com</tt> and <tt>-surf</tt> also work in conjunction
with <tt>-rdf</tt>.<p>
If a run input file is supplied (<tt>-s</tt>) and <tt>-rdf</tt> is set
to <tt>atom</tt>, exclusions defined
-in that file are taken into account when calculating the rdf.
+in that file are taken into account when calculating the RDF.
The option <tt>-cut</tt> is meant as an alternative way to avoid
-intramolecular peaks in the rdf plot.
+intramolecular peaks in the RDF plot.
It is however better to supply a run input file with a higher number of
-exclusions. For eg. benzene a topology with nrexcl set to 5
-would eliminate all intramolecular contributions to the rdf.
+exclusions. For e.g. benzene a topology, setting nrexcl to 5
+would eliminate all intramolecular contributions to the RDF.
Note that all atoms in the selected groups are used, also the ones
that don't have Lennard-Jones interactions.<p>
-Option <tt>-cn</tt> produces the cumulative number rdf,
+Option <tt>-cn</tt> produces the cumulative number RDF,
i.e. the average number of particles within a distance r.<p>
To bridge the gap between theory and experiment structure factors can
be computed (option <tt>-sq</tt>). The algorithm uses FFT, the grid
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.002 </tt> </TD><TD> Binwidth (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> RDF with respect to the center of mass of first group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> RDF with respect to the center of mass of first group </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-surf</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> RDF with respect to the surface of the first group: <tt>no</tt>, <tt>mol</tt> or <tt>res</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rdf</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>atom</tt> </TD><TD> RDF type: <tt>atom</tt>, <tt>mol_com</tt>, <tt>mol_cog</tt>, <tt>res_com</tt> or <tt>res_cog</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize for volume and density </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xy</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use only the x and y components of the distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize for volume and density </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use only the x and y components of the distance </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Shortest distance (nm) to be considered </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of secondary groups to compute RDFs around a central group </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fade</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)^2 to make it go to 1 smoothly. If fade is 0.0 nothing is done. </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_rms compares two structures by computing the root mean square
-deviation (RMSD), the size-independent 'rho' similarity parameter
-(rho) or the scaled rho (rhosc),
-see Maiorov & Crippen, PROTEINS <b>22</b>, 273 (1995).
+<tt>g_rms</tt> compares two structures by computing the root mean square
+deviation (RMSD), the size-independent ρ similarity parameter
+(<tt>rho</tt>) or the scaled ρ (<tt>rhosc</tt>),
+see Maiorov & Crippen, Proteins <b>22</b>, 273 (1995).
This is selected by <tt>-what</tt>.<p>Each structure from a trajectory (<tt>-f</tt>) is compared to a
reference structure. The reference structure
is taken from the structure file (<tt>-s</tt>).<p>
With option <tt>-mir</tt> also a comparison with the mirror image of
the reference structure is calculated.
This is useful as a reference for 'significant' values, see
-Maiorov & Crippen, P
ROTEINS <b>22</b>, 273 (1995).<p>
+Maiorov & Crippen, P
roteins <b>22</b>, 273 (1995).<p>
Option <tt>-prev</tt> produces the comparison with a previous frame
the specified number of frames ago.<p>
Option <tt>-m</tt> produces a matrix in <tt>.<a href="xpm.html">xpm</a></tt> format of
translation), translation only, or no fitting at all.<p>
Option <tt>-mw</tt> controls whether mass weighting is done or not.
If you select the option (default) and
-supply a valid <a href="tpr.html">tpr</a> file masses will be taken from there,
-otherwise the masses will be deduced from the atommass.<a href="dat.html">dat</a> file in
-the GROMACS library directory. This is fine for proteins but not
-necessarily for other molecules. A default mass of 12.011 amu (Carbon)
+supply a valid <tt>.<a href="tpr.html">tpr</a></tt> file masses will be taken from there,
+otherwise the masses will be deduced from the <tt>atommass.<a href="dat.html">dat</a></tt> file in
+<tt>GMXLIB</tt>. This is fine for proteins, but not
+necessarily for other molecules. A default mass of 12.011 amu (carbon)
is assigned to unknown atoms. You can check whether this happend by
turning on the <tt>-debug</tt> flag and inspecting the <a href="log.html">log</a> file.<p>
With <tt>-f2</tt>, the 'other structures' are taken from a second
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-what</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rmsd</tt> </TD><TD> Structural difference measure: <tt>rmsd</tt>, <tt>rho</tt> or <tt>rhosc</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> PBC check </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> PBC check </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rot+trans</tt> </TD><TD> Fit to reference structure: <tt>rot+trans</tt>, <tt>translation</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-prev</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Compare with previous frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split graph where time is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split graph where time is zero </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame to matrix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame to matrix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum level in comparison matrix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Minimum level in comparison matrix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum level in bond angle matrix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Minimum level in bond angle matrix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use mass weighting for superposition </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use mass weighting for superposition </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>80</tt> </TD><TD> Number of levels in the matrices </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to compute RMS between </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsdist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_rmsdist computes the root mean square deviation of atom distances,
+<tt>g_rmsdist</tt> computes the root mean square deviation of atom distances,
which has the advantage that no fit is needed like in standard RMS
-deviation as computed by <a href="g_rms.html">g_rms</a>.
+deviation as computed by <tt><a href="g_rms.html">g_rms</a></tt>.
The reference structure is taken from the structure file.
-The rmsd at time t is calculated as the rms
+The RMSD at time t is calculated as the RMS
of the differences in distance between atom-pairs in the reference
structure and the structure at time t.<p>
-g_rmsdist can also produce matrices of the rms distances, rms distances
+<tt>g_rmsdist</tt> can also produce matrices of the rms distances, rms distances
scaled with the mean distance and the mean distances and matrices with
NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists
of atom pairs with 1/r^3 and 1/r^6 averaged distance below the
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize rms in # levels </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize RMS in this number of levels </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum level in matrices </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sumh</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> average distance over equivalent hydrogens </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions when computing distances </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sumh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average distance over equivalent hydrogens </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions when computing distances </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
-deviation) of atomic positions
-after (optionally) fitting to a reference frame.<p>
+<tt>g_rmsf</tt> computes the root mean square fluctuation (RMSF, i.e. standard
+deviation) of atomic positions in the trajectory (supplied with <tt>-f</tt>)
+after (optionally) fitting to a reference frame
(supplied with <tt>-s</tt>).<p>
With option <tt>-oq</tt> the RMSF values are converted to B-factor
-values, which are written to a <a href="pdb.html">pdb</a> file with the coordinates, of the
-structure file, or of a <a href="pdb.html">pdb</a> file when <tt>-q</tt> is specified.
+values, which are written to a <tt>.<a href="pdb.html">pdb</a></tt> file with the coordinates, of the
+structure file, or of a <tt>.<a href="pdb.html">pdb</a></tt> file when <tt>-q</tt> is specified.
Option <tt>-ox</tt> writes the B-factors to a file with the average
coordinates.<p>
With the option <tt>-od</tt> the root mean square deviation with
respect to the reference structure is calculated.<p>
-With the option <tt>aniso</tt> g_rmsf will compute anisotropic
+With the option <tt>-aniso</tt>, <tt>g_rmsf</tt> will compute anisotropic
temperature factors and then it will also output average coordinates
-and a <a href="pdb.html">pdb</a> file with ANISOU records (corresonding to the <tt>-oq</tt>
+and a <tt>.<a href="pdb.html">pdb</a></tt> file with ANISOU records (corresonding to the <tt>-oq</tt>
or <tt>-ox</tt> option). Please note that the U values
-are orientation dependent, so before comparison with experimental data
+are orientation-dependent, so before comparison with experimental data
you should verify that you fit to the experimental coordinates.<p>
-When a <a href="pdb.html">pdb</a> input file is passed to the program and the <tt>-aniso</tt>
+When a <tt>.<a href="pdb.html">pdb</a></tt> input file is passed to the program and the <tt>-aniso</tt>
flag is set
a correlation plot of the Uij will be created, if any anisotropic
-temperature factors are present in the <
a href="pdb.html">pdb</a> file.<p>
+temperature factors are present in the <
tt>.<a href="pdb.html">pdb</a></tt> file.<p>
With option <tt>-dir</tt> the average MSF (3x3) matrix is diagonalized.
This shows the directions in which the atoms fluctuate the most and
the least.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]res</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate averages for each residue </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]aniso</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute anisotropic termperature factors </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]res</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate averages for each residue </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aniso</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute anisotropic termperature factors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match. </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rotacf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_rotacf calculates the rotational correlation function
-for molecules. Three atoms (i,j,k) must be given in the index
-file, defining two vectors ij and jk. The rotational acf
+<tt>g_rotacf</tt> calculates the rotational correlation function
+for molecules. Atom triplets (i,j,k) must be given in the index
+file, defining two vectors ij and jk. The rotational ACF
is calculated as the autocorrelation function of the vector
n = ij x jk, i.e. the cross product of the two vectors.
Since three atoms span a plane, the order of the three atoms
-does not matter. Optionally, controlled by the -d switch, you can
+does not matter. Optionally, by invoking the <tt>-d</tt> switch, you can
calculate the rotational correlation function for linear molecules
-by specifying two atoms (i,j) in the index file.
+by specifying atom pairs (i,j) in the index file.
<p>
EXAMPLES<p>
-g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1
--fa expfit-x-P1 -beginfit 2.5 -endfit 20.0<p>
+<tt>g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1
+-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0</tt><p>
This will calculate the rotational correlation function using a first
order Legendre polynomial of the angle of a vector defined by the index
-file. The correlation function will be fitted from 2.5 ps till 20.0 ps
-to a two parameter exponential.
-
+file. The correlation function will be fitted from 2.5 ps until 20.0 ps
+to a two-parameter exponential.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use index doublets (vectors) for correlation function instead of triplets (planes) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average over molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use index doublets (vectors) for correlation function instead of triplets (planes) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average over molecules </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rotmat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_rotmat plots the rotation matrix required for least squares fitting
+<tt>g_rotmat</tt> plots the rotation matrix required for least squares fitting
a conformation onto the reference conformation provided with
<tt>-s</tt>. Translation is removed before fitting.
The output are the three vectors that give the new directions
determining the orientation of a molecule
at an interface, possibly on a trajectory produced with
<tt><a href="trjconv.html">trjconv</a> -fit rotxy+transxy</tt> to remove the rotation
-in the xy-plane.
+in the <it>x-y</it> plane.
<p>
Option <tt>-ref</tt> determines a reference structure for fitting,
instead of using the structure from <tt>-s</tt>. The structure with
the lowest sum of RMSD's to all other structures is used.
Since the computational cost of this procedure grows with
the square of the number of frames, the <tt>-skip</tt> option
-can be useful. A full fit or only a fit in the x/y plane can
+can be useful. A full fit or only a fit in the <it>x-y</it> plane can
be performed.
<p>
-Option <tt>-fitxy</tt> fits in the x/y plane before determining
+Option <tt>-fitxy</tt> fits in the <it>x-y</it> plane before determining
the rotation matrix.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ref</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Determine the optimal reference structure: <tt>none</tt>, <tt>xyz</tt> or <tt>xy</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Use every nr-th frame for -ref </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fitxy</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Fit the x/y rotation before determining the rotation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use mass weighted fitting </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Use every nr-th frame for <tt>-ref</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fitxy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Fit the x/y rotation before determining the rotation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use mass weighted fitting </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_saltbr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_saltbr plots the distance between all combination of charged groups
+<tt>g_saltbr</tt> plots the distance between all combination of charged groups
as a function of time. The groups are combined in different ways.
-A minimum distance can be given, (eg. the cut-off), then groups
-that are never closer than that distance will not be plotted.<br>
-Output will be in a number of fixed filenames, min-min.<a href="xvg.html">xvg</a>, plus-min.<a href="xvg.html">xvg</a>
-and plus-plus.<a href="xvg.html">xvg</a>, or files for every individual ion-pair if the <tt>-sep</tt>
-option is selected. In this case files are named as <tt>sb-ResnameResnr-Atomnr</tt>.
-There may be many such files.
+A minimum distance can be given (i.e. a cut-off), such that groups
+that are never closer than that distance will not be plotted.<p>
+Output will be in a number of fixed filenames, <tt>min-min.<a href="xvg.html">xvg</a></tt>, <tt>plus-min.<a href="xvg.html">xvg</a></tt>
+and <tt>plus-plus.<a href="xvg.html">xvg</a></tt>, or files for every individual ion pair if the <tt>-sep</tt>
+option is selected. In this case, files are named as <tt>sb-(Resname)(Resnr)-(Atomnr)</tt>.
+There may be <b>many</b> such files.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000 </tt> </TD><TD> trunc distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use separate files for each interaction (may be MANY) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000 </tt> </TD><TD> Groups that are never closer than this distance are not plotted </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use separate files for each interaction (may be MANY) </TD></TD>
</TABLE>
<P>
<hr>
--- /dev/null
+<HTML>
+<HEAD>
+<TITLE>g_sans</TITLE>
+<LINK rel=stylesheet href="style.css" type="text/css">
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
+<TABLE WIDTH="98%" NOBORDER >
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
+<TD WIDTH=116>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sans</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
+<HR>
+<H3>Description</H3>
+<p>
+This is simple tool to compute SANS spectra using Debye formula
+It currently uses topology file (since it need to assigne element for each atom)
+<p>
+Parameters:<p><tt>-pr</tt> Computes normalized g(r) function averaged over trajectory<p>
+<tt>-prframe</tt> Computes normalized g(r) function for each frame<p>
+<tt>-sq</tt> Computes SANS intensity curve averaged over trajectory<p>
+<tt>-sqframe</tt> Computes SANS intensity curve for each frame<p>
+<tt>-startq</tt> Starting q value in nm<p>
+<tt>-endq</tt> Ending q value in nm<p>
+<tt>-qstep</tt> Stepping in q space<p>
+Note: When using Debye direct method computational cost increases as
+1/2 * N * (N - 1) where N is atom number in group of interest
+<p>
+WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!
+<P>
+<H3>Files</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">nsfactor.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pr.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-sq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sq.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-prframe</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> prframe.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-sqframe</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sqframe.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+</TABLE>
+<P>
+<H3>Other options</H3>
+<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
+<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mode</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>direct</tt> </TD><TD> Mode for sans spectra calculation: <tt>direct</tt> or <tt>mc</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mcover</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Monte-Carlo coverage should be -1(default) or (0,1] </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions for computing distances </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-startq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Starting q (1/nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>2 </tt> </TD><TD> Ending q (1/nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-qstep</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.01 </tt> </TD><TD> Stepping in q (1/nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Random seed for Monte-Carlo </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nt</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>8</tt> </TD><TD> Number of threads to start </TD></TD>
+</TABLE>
+<P>
+<hr>
+<div ALIGN=RIGHT>
+<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
+<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
+</div>
+</BODY>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sas</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area.
-As a side effect the Connolly surface can be generated as well in
-a <a href="pdb.html">pdb</a> file where the nodes are represented as atoms and the vertices
-connecting the nearest nodes as CONECT records.
+<tt>g_sas</tt> computes hydrophobic, hydrophilic and total solvent
+accessible surface area. See Eisenhaber F, Lijnzaad P, Argos P,
+Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284.
+As a side effect, the Connolly surface can be generated as well in
+a <tt>.<a href="pdb.html">pdb</a></tt> file where the nodes are represented as atoms and the
+vertice connecting the nearest nodes as CONECT records.
The program will ask for a group for the surface calculation
and a group for the output. The calculation group should always
consists of all the non-solvent atoms in the system.
The output group can be the whole or part of the calculation group.
-The area can be plotted
+The average and standard deviation of the area over the trajectory can be plotted
per residue and atom as well (options <tt>-or</tt> and <tt>-oa</tt>).
-In combination with the latter option an <tt><a href="itp.html">itp</a></tt> file can be
+In combination with the latter option an <tt>
.<a href="itp.html">itp</a></tt> file can be
generated (option <tt>-i</tt>)
which can be used to restrain surface atoms.<p>
By default, periodic boundary conditions are taken into account,
this can be turned off using the <tt>-nopbc</tt> option.<p>
-With the <tt>-tv</tt> option the total volume and density of the molecule can be
-computed.
+With the <tt>-tv</tt> option the total volume and density of the
+molecule can be computed.
Please consider whether the normal probe radius is appropriate
in this case or whether you would rather use e.g. 0. It is good
to keep in mind that the results for volume and density are very
-approximate, in e.g. ice Ih one can easily fit water molecules in the
-pores which would yield too low volume, too high surface area and too
-high density.
+approximate. For example, in ice Ih, one can easily fit water molecules in the
+pores which would yield a volume that is too low, and surface area and density
+that are both too high.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-probe</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.14 </tt> </TD><TD> Radius of the solvent probe (nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ndots</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>24</tt> </TD><TD> Number of dots per sphere, more dots means more accuracy </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-qmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.2 </tt> </TD><TD> The maximum charge (e, absolute value) of a hydrophobic atom </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]f_index</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Determine from a group in the index file what are the hydrophobic atoms rather than from the charge </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]f_index</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Determine from a group in the index file what are the hydrophobic atoms rather than from the charge </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-minarea</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Take periodicity into account </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]prot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Output the protein to the connelly <a href="pdb.html">pdb</a> file too </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dgs</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> default value for solvation free energy per area (kJ/mol/nm^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Take periodicity into account </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]prot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Output the protein to the Connelly <tt>.<a href="pdb.html">pdb</a></tt> file too </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dgs</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Default value for solvation free energy per area (kJ/mol/nm^2) </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_select</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_select writes out basic data about dynamic selections.
+<tt>g_select</tt> writes out basic data about dynamic selections.
It can be used for some simple analyses, or the output can
be combined with output from other programs and/or external
analysis programs to calculate more complex things.
Any combination of the output options is possible, but note
-that <tt>-om</tt> only operates on the first selection.<p>
+that <tt>-om</tt> only operates on the first selection.
+<tt>-os</tt> is the default output option if none is selected.<p>
With <tt>-os</tt>, calculates the number of positions in each
selection for each frame. With <tt>-norm</tt>, the output is
between 0 and 1 and describes the fraction from the maximum
of positions is omitted from the output. In this case, only one
selection can be given.<p>
With <tt>-on</tt>, the selected atoms are written as a index file
-compatible with <a href="make_<a href="ndx.html">ndx</a>.html">make_<a href="ndx.html">ndx</a></a> and the analyzing tools. Each selection
+compatible with <tt><a href="make_<a href="ndx.html">ndx</a>.html">make_<a href="ndx.html">ndx</a></a></tt> and the analyzing tools. Each selection
is written as a selection group and for dynamic selections a
group is written for each frame.<p>
For residue numbers, the output of <tt>-oi</tt> can be controlled
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmpbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Make molecules whole for each frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions for distance calculation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-select</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Selection string (use 'help' for help) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmpbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Make molecules whole for each frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions for distance calculation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-select</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Selection string (use 'help' for help). Note that the whole selection string will need to be quoted so that your shell will pass it in as a string. Example: <tt>g_select -select '"Nearby water" resname SOL and within 0.25 of group Protein'</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-selrpos</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>atom</tt> </TD><TD> Selection reference position: <tt>atom</tt>, <tt>res_com</tt>, <tt>res_cog</tt>, <tt>mol_com</tt>, <tt>mol_cog</tt>, <tt>whole_res_com</tt>, <tt>whole_res_cog</tt>, <tt>whole_mol_com</tt>, <tt>whole_mol_cog</tt>, <tt>part_res_com</tt>, <tt>part_res_cog</tt>, <tt>part_mol_com</tt>, <tt>part_mol_cog</tt>, <tt>dyn_res_com</tt>, <tt>dyn_res_cog</tt>, <tt>dyn_mol_com</tt> or <tt>dyn_mol_cog</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seltype</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>atom</tt> </TD><TD> Default analysis positions: <tt>atom</tt>, <tt>res_com</tt>, <tt>res_cog</tt>, <tt>mol_com</tt>, <tt>mol_cog</tt>, <tt>whole_res_com</tt>, <tt>whole_res_cog</tt>, <tt>whole_mol_com</tt>, <tt>whole_mol_cog</tt>, <tt>part_res_com</tt>, <tt>part_res_cog</tt>, <tt>part_mol_com</tt>, <tt>part_mol_cog</tt>, <tt>dyn_res_com</tt>, <tt>dyn_res_cog</tt>, <tt>dyn_mol_com</tt> or <tt>dyn_mol_cog</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]dump</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do not print the frame time (-om, -oi) or the index size (-oi) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Normalize by total number of positions with -os </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]cfnorm</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Normalize by covered fraction with -os </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]dump</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do not print the frame time (-om, -oi) or the index size (-oi) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Normalize by total number of positions with -os </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cfnorm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Normalize by covered fraction with -os </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-resnr</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>number</tt> </TD><TD> Residue number output type: <tt>number</tt> or <tt>index</tt> </TD></TD>
</TABLE>
<P>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sgangle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
Compute the angle and distance between two groups.
The groups are defined by a number of atoms given in an index file and
may be two or three atoms in size.
-If -one is set, only one group should be specified in the index
+If <tt>-one</tt> is set, only one group should be specified in the index
file and the angle between this group at time 0 and t will be computed.
The angles calculated depend on the order in which the atoms are
-given. Giving for instance 5 6 will rotate the vector 5-6 with
+given. Giving, for instance, 5 6 will rotate the vector 5-6 with
180 degrees compared to giving 6 5. <p>If three atoms are given,
the normal on the plane spanned by those three atoms will be
calculated, using the formula P1P2 x P1P3.
The cos of the angle is calculated, using the inproduct of the two
normalized vectors.<p>
Here is what some of the file options do:<br>
--oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.<br>
--od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.<br>
--od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.<br>
--od2: For two planes this option has no meaning.
+<tt>-oa</tt>: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.<br>
+<tt>-od</tt>: Distance between two groups. Distance is taken from the center of one group to the center of the other group.<br>
+<tt>-od1</tt>: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.<br>
+<tt>-od2</tt>: For two planes this option has no meaning.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only one group compute angle between vector at time zero and time t </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the Z-axis as reference </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only one group compute angle between vector at time zero and time t </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the <it>z</it>-axis as reference </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sham</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_sham makes multi-dimensional free-energy, enthalpy and entropy plots.
-g_sham reads one or more <a href="xvg.html">xvg</a> files and analyzes data sets.
-g_sham basic purpose is plotting Gibbs free energy landscapes
+<tt>g_sham</tt> makes multi-dimensional free-energy, enthalpy and entropy plots.
+<tt>g_sham</tt> reads one or more <tt>.<a href="xvg.html">xvg</a></tt> files and analyzes data sets.
+The basic purpose of <tt>g_sham</tt> is to plot Gibbs free energy landscapes
(option <tt>-ls</tt>)
-by Bolzmann inverting multi-dimensional histograms (option <tt>-lp</tt>)
+by Bolzmann inverting multi-dimensional histograms (option <tt>-lp</tt>),
but it can also
make enthalpy (option <tt>-lsh</tt>) and entropy (option <tt>-lss</tt>)
plots. The histograms can be made for any quantities the user supplies.
A line in the input file may start with a time
-(see option <tt>-time</tt>) and any number of y values may follow.
+(see option <tt>-time</tt>) and any number of <it>y</it>-values may follow.
Multiple sets can also be
read when they are separated by & (option <tt>-n</tt>),
-in this case only one y value is read from each line.
+in this case only one <it>y</it>-value is read from each line.
All lines starting with # and @ are skipped.
<p>
Option <tt>-ge</tt> can be used to supply a file with free energies
<p>
Option <tt>-<a href="ene.html">ene</a></tt> can be used to supply a file with energies.
These energies are used as a weighting function in the single
-histogram analysis method due to Kumar et. al. When also temperatures
-are supplied (as a second column in the file) an experimental
+histogram analysis method by Kumar et al. When temperatures
+are supplied (as a second column in the file), an experimental
weighting scheme is applied. In addition the vales
are used for making enthalpy and entropy plots.
<p>
-With option <tt>-dim</tt> dimensions can be gives for distances.
+With option <tt>-dim</tt>, dimensions can be gives for distances.
When a distance is 2- or 3-dimensional, the circumference or surface
sampled by two particles increases with increasing distance.
Depending on what one would like to show, one can choose to correct
the histogram and free-energy for this volume effect.
-The probability is normalized by r and r^2 for a dimension of 2 and 3
+The probability is normalized by r and r^2 for dimensions of 2 and 3,
respectively.
A value of -1 is used to indicate an angle in degrees between two
vectors: a sin(angle) normalization will be applied.
-Note that for angles between vectors the inner-product or cosine
+<b>Note</b> that for angles between vectors the inner-product or cosine
is the natural quantity to use, as it will produce bins of the same
volume.
<P>
<TR><TD ALIGN=RIGHT> <b><tt>-lss</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> entropy.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-map</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> map.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ls3</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> gibbs3.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-mdata</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> mapdata.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mdata</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> mapdata.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> shamlog.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Expect a time in the input </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Expect a time in the input </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> First time to read from set </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Last time to read from set </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ttol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Tolerance on time in appropriate units (usually ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read # sets separated by & </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the derivative </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read this number of sets separated by lines containing only an ampersand </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the derivative </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Binwidth for the distribution </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sham</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Turn off energy weighting even if energies are given </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sham</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Turn off energy weighting even if energies are given </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tsham</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for single histogram analysis </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-pmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum probability. Anything lower than this will be set to zero </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dim</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last) </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sigeps</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-Sigeps is a simple utility that converts c6/c12 or c6/cn combinations
-to sigma and epsilon, or vice versa. It can also plot the potential
-in file. In addition it makes an approximation of a Buckingham potential
-to a Lennard Jones potential.
+<tt>g_sigeps</tt> is a simple utility that converts C6/C12 or C6/Cn combinations
+to σ and ε, or vice versa. It can also plot the potential
+in file. In addition, it makes an approximation of a Buckingham potential
+to a Lennard-Jones potential.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-c6</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> c6 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-cn</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1e-06 </tt> </TD><TD> constant for repulsion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-pow</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>12</tt> </TD><TD> power of the repulsion term </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sig</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.3 </tt> </TD><TD> sig </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eps</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> <a href="eps.html">eps</a> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-c6</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> C6 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cn</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1e-06 </tt> </TD><TD> Constant for repulsion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pow</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>12</tt> </TD><TD> Power of the repulsion term </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sig</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.3 </tt> </TD><TD> σ </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eps</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> ε </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-A</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>100000</tt> </TD><TD> Buckingham A </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-B</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>32 </tt> </TD><TD> Buckingham B </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-C</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Buckingham C </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-qi</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> qi </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-qj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> qj </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sigfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.7 </tt> </TD><TD> Factor in front of sigma for starting the plot </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sigfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.7 </tt> </TD><TD> Factor in front of σ for starting the plot </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sorient</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_sorient analyzes solvent orientation around solutes.
+<tt>g_sorient</tt> analyzes solvent orientation around solutes.
It calculates two angles between the vector from one or more
-reference positions to the first atom of each solvent molecule:<br>
-theta1: the angle with the vector from the first atom of the solvent
+reference positions to the first atom of each solvent molecule:<p>
+θ_1: the angle with the vector from the first atom of the solvent
molecule to the midpoint between atoms 2 and 3.<br>
-theta2: the angle with the normal of the solvent plane, defined by the
-same three atoms, or when the option <tt>-v23</tt> is set
-the angle with the vector between atoms 2 and 3.<br>
+θ_2: the angle with the normal of the solvent plane, defined by the
+same three atoms, or, when the option <tt>-v23</tt> is set,
+the angle with the vector between atoms 2 and 3.<p>
The reference can be a set of atoms or
the center of mass of a set of atoms. The group of solvent atoms should
consist of 3 atoms per solvent molecule.
Only solvent molecules between <tt>-rmin</tt> and <tt>-rmax</tt> are
considered for <tt>-o</tt> and <tt>-no</tt> each frame.<p>
-<tt>-o</tt>: distribtion of cos(
theta1) for rmin<=r<=rmax.<p>
-<tt>-no</tt>: distribution of cos(
theta2) for rmin<=r<=rmax.<p>
-<tt>-ro</tt>: <cos(theta1)> and <3cos^2(theta2)-1> as a function of the
+<tt>-o</tt>: distribtion of cos(
θ_1) for rmin<=r<=rmax.<p>
+<tt>-no</tt>: distribution of cos(
θ_2) for rmin<=r<=rmax.<p>
+<tt>-ro</tt>: <cos(θ_1)> and <3cos(^2θ_2)-1> as a function of the
distance.<p>
<tt>-co</tt>: the sum over all solvent molecules within distance r
-of cos(
theta1) and 3cos^2(theta2)-1 as a function of r.<p>
+of cos(
θ_1) and 3cos(^2(θ_2)-1) as a function of r.<p>
<tt>-rc</tt>: the distribution of the solvent molecules as a function of r
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the center of mass as the reference postion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v23</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the vector between atoms 2 and 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the center of mass as the reference postion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v23</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the vector between atoms 2 and 3 </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum distance (nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> Maximum distance (nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02 </tt> </TD><TD> Binwidth for the cosine </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02 </tt> </TD><TD> Binwidth for r (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_spatial</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_spatial calculates the spatial distribution function and
+<tt>g_spatial</tt> calculates the spatial distribution function and
outputs it in a form that can be read by VMD as Gaussian98 cube format.
-This was developed from template.c (gromacs-3.3).
-For a system of 32K atoms and a 50ns trajectory, the SDF can be generated
+This was developed from template.c (GROMACS-3.3).
+For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated
in about 30 minutes, with most of the time dedicated to the two runs through
-<a href="trjconv.html">trjconv</a> that are required to center everything properly.
-This also takes a whole bunch of space (3 copies of the <a href="xtc.html">xtc</a> file).
+<tt><a href="trjconv.html">trjconv</a></tt> that are required to center everything properly.
+This also takes a whole bunch of space (3 copies of the <tt>.<a href="xtc.html">xtc</a></tt> file).
Still, the pictures are pretty and very informative when the fitted selection is properly made.
-3-4 atoms in a widely mobile group like a free amino acid in solution works
+3-4 atoms in a widely mobile group (like a free amino acid in solution) works
well, or select the protein backbone in a stable folded structure to get the SDF
of solvent and look at the time-averaged solvation shell.
-It is also possible using this program to generate the SDF based on some arbitrarty
-Cartesian coordinate. To do that, simply omit the preliminary <a href="trjconv.html">trjconv</a> steps.
+It is also possible using this program to generate the SDF based on some arbitrary
+Cartesian coordinate. To do that, simply omit the preliminary <tt><a href="trjconv.html">trjconv</a></tt> steps.
USAGE:
-1. Use <a href="make_<a href="ndx.html">ndx</a>.html">make_<a href="ndx.html">ndx</a></a> to create a group containing the atoms around which you want the SDF
+1. Use <tt><a href="make_<a href="ndx.html">ndx</a>.html">make_<a href="ndx.html">ndx</a></a></tt> to create a group containing the atoms around which you want the SDF
-2. <a href="trjconv.html">trjconv</a> -s a.<a href="tpr.html">tpr</a> -f a.<a href="xtc.html">xtc</a> -o b.<a href="xtc.html">xtc</a> -center tric -ur compact -pbc none
+2. <tt><a href="trjconv.html">trjconv</a> -s a.<a href="tpr.html">tpr</a> -f a.<a href="xtc.html">xtc</a> -o b.<a href="xtc.html">xtc</a> -center tric -ur compact -pbc none</tt>
-3. <a href="trjconv.html">trjconv</a> -s a.<a href="tpr.html">tpr</a> -f b.<a href="xtc.html">xtc</a> -o c.<a href="xtc.html">xtc</a> -fit rot+trans
+3. <tt><a href="trjconv.html">trjconv</a> -s a.<a href="tpr.html">tpr</a> -f b.<a href="xtc.html">xtc</a> -o c.<a href="xtc.html">xtc</a> -fit rot+trans</tt>
-4. run g_spatial on the <a href="xtc.html">xtc</a> output of step #3.
+4. run <tt>g_spatial</tt> on the <tt>.<a href="xtc.html">xtc</a></tt> output of step #3.
-5. Load grid.cube into VMD and view as an isosurface.
+5. Load <tt>grid.cube</tt> into VMD and view as an isosurface.
-*** Systems such as micelles will require <a href="trjconv.html">trjconv</a> -pbc cluster between steps 1 and 2
-
-WARNINGS:
+<b>Note</b> that systems such as micelles will require <tt><a href="trjconv.html">trjconv</a> -pbc cluster</tt> between steps 1 and 2
+WARNINGS:<br>
The SDF will be generated for a cube that contains all bins that have some non-zero occupancy.
-However, the preparatory -fit rot+trans option to <a href="trjconv.html">trjconv</a> implies that your system will be rotating
+However, the preparatory <tt>-fit rot+trans</tt> option to <tt><a href="trjconv.html">trjconv</a></tt> implies that your system will be rotating
and translating in space (in order that the selected group does not). Therefore the values that are
returned will only be valid for some region around your central group/coordinate that has full overlap
with system volume throughout the entire translated/rotated system over the course of the trajectory.
It is up to the user to ensure that this is the case.
-BUGS:
-
+BUGS:<br>
When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected
-and the program is halted prior to the fault while displaying a warning message suggesting the use of the -nab
+and the program is halted prior to the fault while displaying a warning message suggesting the use of the <tt>-nab</tt> (Number of Additional Bins)
option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again
-with an increased -nab value.
-
-RISKY OPTIONS:
+with an increased <tt>-nab</tt> value.
+RISKY OPTIONS:<br>
To reduce the amount of space and time required, you can output only the coords
-that are going to be used in the first and subsequent run through <a href="trjconv.html">trjconv</a>.
-However, be sure to set the -nab option to a sufficiently high value since
-memory is allocated for cube bins based on the initial coords and the -nab
-(Number of Additional Bins) option value.
+that are going to be used in the first and subsequent run through <tt><a href="trjconv.html">trjconv</a></tt>.
+However, be sure to set the <tt>-nab</tt> option to a sufficiently high value since
+memory is allocated for cube bins based on the initial coordinates and the <tt>-nab</tt>
+option value.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use periodic boundary conditions for computing distances </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]div</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE (-nodiv) to get accurate counts per frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use periodic boundary conditions for computing distances </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]div</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE (<tt>-nodiv</tt>) to get accurate counts per frame </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ign</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.05 </tt> </TD><TD> Width of the bins in nm </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.05 </tt> </TD><TD> Width of the bins (nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nab</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>4</tt> </TD><TD> Number of additional bins to ensure proper memory allocation </TD></TD>
</TABLE>
<P>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_spol</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_spol analyzes dipoles around a solute; it is especially useful
+<tt>g_spol</tt> analyzes dipoles around a solute; it is especially useful
for polarizable water. A group of reference atoms, or a center
of mass reference (option <tt>-com</tt>) and a group of solvent
atoms is required. The program splits the group of solvent atoms
the inner product of the distance vector
and the dipole of the solvent molecule is determined.
For solvent molecules with net charge (ions), the net charge of the ion
-is subtracted evenly at all atoms in the selection of each ion.
+is subtracted evenly from all atoms in the selection of each ion.
The average of these dipole components is printed.
The same is done for the polarization, where the average dipole is
subtracted from the instantaneous dipole. The magnitude of the average
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the center of mass as the reference postion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the center of mass as the reference postion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-refat</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The reference atom of the solvent molecule </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance (nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.32 </tt> </TD><TD> Maximum distance (nm) </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_tcaf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_tcaf computes tranverse current autocorrelations.
-These are used to estimate the shear viscosity eta.
+<tt>g_tcaf</tt> computes tranverse current autocorrelations.
+These are used to estimate the shear viscosity, η.
For details see: Palmer, Phys. Rev. E 49 (1994) pp 359-366.<p>
Transverse currents are calculated using the
-k-vectors (1,0,0) and (2,0,0) each also in the y- and z-direction,
+k-vectors (1,0,0) and (2,0,0) each also in the <it>y</it>- and <it>z</it>-direction,
(1,1,0) and (1,-1,0) each also in the 2 other planes (these vectors
are not independent) and (1,1,1) and the 3 other box diagonals (also
not independent). For each k-vector the sine and cosine are used, in
combination with the velocity in 2 perpendicular directions. This gives
a total of 16*2*2=64 transverse currents. One autocorrelation is
-calculated fitted for each k-vector, which gives 16 tcaf's. Each of
-these tcaf's is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)),
-v = -t/(2 tau), W = sqrt(1 - 4 tau eta/rho k^2), which gives 16 tau's
-and eta's. The fit weights decay with time as exp(-t/wt), the tcaf and
-fit are calculated up to time 5*wt.
-The eta's should be fitted to 1 - a eta(k) k^2, from which
+calculated fitted for each k-vector, which gives 16 TCAFs. Each of
+these TCAFs is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)),
+v = -t/(2 τ), W = sqrt(1 - 4 τ η/ρ k^2), which gives 16 values of τ
+and η. The fit weights decay exponentially with time constant w (given with <tt>-wt</tt>) as exp(-t/w), and the TCAF and
+fit are calculated up to time 5*w.
+The η values should be fitted to 1 - a η(k) k^2, from which
one can estimate the shear viscosity at k=0.<p>
When the box is cubic, one can use the option <tt>-oc</tt>, which
-averages the tcaf's over all k-vectors with the same length.
-This results in more accurate tcaf's.
-Both the cubic tcaf's and fits are written to <tt>-oc</tt>
-The cubic
eta estimates are also written to <tt>-ov</tt>.<p>
-With option <tt>-mol</tt> the transverse current is determined of
-molecules instead of atoms. In this case the index group should
+averages the TCAFs over all k-vectors with the same length.
+This results in more accurate TCAFs.
+Both the cubic TCAFs and fits are written to <tt>-oc</tt>
+The cubic
η estimates are also written to <tt>-ov</tt>.<p>
+With option <tt>-mol</tt>, the transverse current is determined of
+molecules instead of atoms. In this case, the index group should
consist of molecule numbers instead of atom numbers.<p>
The k-dependent viscosities in the <tt>-ov</tt> file should be
-fitted to eta(k) = eta0 (1 - a k^2) to obtain the viscosity at
+fitted to η(k) = η_0 (1 - a k^2) to obtain the viscosity at
infinite wavelength.<p>
-NOTE: make sure you write coordinates and velocities often enough.
+<b>Note:</b> make sure you write coordinates and velocities often enough.
The initial, non-exponential, part of the autocorrelation function
is very important for obtaining a good fit.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate tcaf of molecules </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]k34</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Also use k=(3,0,0) and k=(4,0,0) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate TCAF of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]k34</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Also use k=(3,0,0) and k=(4,0,0) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-wt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Exponential decay time for the TCAF fit weights </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_traj</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_traj plots coordinates, velocities, forces and/or the box.
+<tt>g_traj</tt> plots coordinates, velocities, forces and/or the box.
With <tt>-com</tt> the coordinates, velocities and forces are
calculated for the center of mass of each group.
When <tt>-mol</tt> is set, the numbers in the index file are
provided velocities are present in the trajectory file.
This implies <tt>-com</tt>.<p>
Options <tt>-cv</tt> and <tt>-cf</tt> write the average velocities
-and average forces as temperature factors to a <a href="pdb.html">pdb</a> file with
-the average coordinates. The temperature factors are scaled such
-that the maximum is 10. The scaling can be changed with the option
-<tt>-scale</tt>. To get the velocities or forces of one
+and average forces as temperature factors to a <tt>.<a href="pdb.html">pdb</a></tt> file with
+the average coordinates or the coordinates at <tt>-ctime</tt>.
+The temperature factors are scaled such that the maximum is 10.
+The scaling can be changed with the option <tt>-scale</tt>.
+To get the velocities or forces of one
frame set both <tt>-b</tt> and <tt>-e</tt> to the time of
desired frame. When averaging over frames you might need to use
the <tt>-nojump</tt> option to obtain the correct average coordinates.
If you select either of these option the average force and velocity
-for each atom are written to an <a href="xvg.html">xvg</a> file as well
+for each atom are written to an <tt>.<a href="xvg.html">xvg</a></tt> file as well
(specified with <tt>-av</tt> or <tt>-af</tt>).<p>
Option <tt>-vd</tt> computes a velocity distribution, i.e. the
norm of the vector is plotted. In addition in the same graph
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot data for the com of each group </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Make molecules whole for COM </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Index contains molecule numbers iso atom numbers </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove jumps of atoms across the box </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]x</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot X-component </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]y</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot Y-component </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot Z-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot data for the com of each group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Make molecules whole for COM </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Index contains molecule numbers iso atom numbers </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove jumps of atoms across the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]x</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot X-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]y</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot Y-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot Z-component </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to consider </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]len</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot vector length </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Full precision output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]len</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot vector length </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Full precision output </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Binwidth for velocity histogram (nm/ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Scale factor for <a href="pdb.html">pdb</a> output, 0 is autoscale </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ctime</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Use frame at this time for x in <tt>-cv</tt> and <tt>-cf</tt> instead of the average x </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Scale factor for <tt>.<a href="pdb.html">pdb</a></tt> output, 0 is autoscale </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_tune_pme</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-For a given number <tt>-np</tt> or <tt>-nt</tt> of processors/threads, this program systematically
-times <a href="mdrun.html">mdrun</a> with various numbers of PME-only nodes and determines
+For a given number <tt>-np</tt> or <tt>-ntmpi</tt> of processors/threads, this program systematically
+times <tt><a href="mdrun.html">mdrun</a></tt> with various numbers of PME-only nodes and determines
which setting is fastest. It will also test whether performance can
be enhanced by shifting load from the reciprocal to the real space
part of the Ewald sum.
-Simply pass your <tt>.<a href="tpr.html">tpr</a></tt> file to g_tune_pme together with other options
-for <
a href="mdrun.html">mdrun</a> as needed.<p>
+Simply pass your <tt>.<a href="tpr.html">tpr</a></tt> file to <tt>g_tune_pme</tt> together with other options
+for <
tt><a href="mdrun.html">mdrun</a></tt> as needed.<p>
Which executables are used can be set in the environment variables
MPIRUN and MDRUN. If these are not present, 'mpirun' and '<a href="mdrun.html">mdrun</a>'
will be used as defaults. Note that for certain MPI frameworks you
need to provide a machine- or hostfile. This can also be passed
-via the MPIRUN variable, e.g.
-
'export MPIRUN="/usr/local/mpirun -machinefile hosts"'<p>
-Please call g_tune_pme with the normal options you would pass to
-<a href="mdrun.html">mdrun</a> and add <tt>-np</tt> for the number of processors to perform the
-tests on, or <tt>-nt</tt> for the number of threads. You can also add <tt>-r</tt>
+via the MPIRUN variable, e.g.<p>
+
<tt>export MPIRUN="/usr/local/mpirun -machinefile hosts"</tt><p>
+Please call <tt>g_tune_pme</tt> with the normal options you would pass to
+<tt><a href="mdrun.html">mdrun</a></tt> and add <tt>-np</tt> for the number of processors to perform the
+tests on, or <tt>-ntmpi</tt> for the number of threads. You can also add <tt>-r</tt>
to repeat each test several times to get better statistics. <p>
-g_tune_pme can test various real space / reciprocal space workloads
+<tt>g_tune_pme</tt> can test various real space / reciprocal space workloads
for you. With <tt>-ntpr</tt> you control how many extra <tt>.<a href="tpr.html">tpr</a></tt> files will be
-written with enlarged cutoffs and smaller fourier grids respectively.
-Typically, the first test (no. 0) will be with the settings from the input
-<tt>.<a href="tpr.html">tpr</a></tt> file; the last test (no. <tt>ntpr</tt>) will have cutoffs multiplied
-by (and at the same time fourier grid dimensions divided by) the scaling
-factor <tt>-fac</tt> (default 1.2). The remaining <tt>.<a href="tpr.html">tpr</a></tt> files will have equally
-spaced values inbetween these extremes. Note that you can set <tt>-ntpr</tt> to 1
-if you just want to find the optimal number of PME-only nodes; in that case
+written with enlarged cutoffs and smaller Fourier grids respectively.
+Typically, the first test (number 0) will be with the settings from the input
+<tt>.<a href="tpr.html">tpr</a></tt> file; the last test (number <tt>ntpr</tt>) will have the Coulomb cutoff
+specified by <tt>-rmax</tt> with a somwhat smaller PME grid at the same time.
+In this last test, the Fourier spacing is multiplied with <tt>rmax</tt>/rcoulomb.
+The remaining <tt>.<a href="tpr.html">tpr</a></tt> files will have equally-spaced Coulomb radii (and Fourier spacings) between these extremes. <b>Note</b> that you can set <tt>-ntpr</tt> to 1
+if you just seek the optimal number of PME-only nodes; in that case
your input <tt>.<a href="tpr.html">tpr</a></tt> file will remain unchanged.<p>
For the benchmark runs, the default of 1000 time steps should suffice for most
MD systems. The dynamic load balancing needs about 100 time steps
to adapt to local load imbalances, therefore the time step counters
-are by default reset after 100 steps. For large systems
-(>1M atoms) you may have to set <tt>-resetstep</tt> to a higher value.
+are by default reset after 100 steps. For large systems (>1M atoms), as well as
+for a higher accuarcy of the measurements, you should set <tt>-resetstep</tt> to a higher value.
From the 'DD' load imbalance entries in the md.<a href="log.html">log</a> output file you
-can tell after how many steps the load is sufficiently balanced.
<p>Example call: <tt>g_tune_pme -np 64 -s protein.<a href="tpr.html">tpr</a> -launch</tt><p>
-After calling <a href="mdrun.html">mdrun</a> several times, detailed performance information
-is available in the output file perf.out.
-Note that during the benchmarks a couple of temporary files are written
-(options
-b*), these will be automatically deleted after each test.<p>
+can tell after how many steps the load is sufficiently balanced.
Example call:<p><tt>g_tune_pme -np 64 -s protein.<a href="tpr.html">tpr</a> -launch</tt><p>
+After calling <tt><a href="mdrun.html">mdrun</a></tt> several times, detailed performance information
+is available in the output file <tt>perf.out.</tt>
+<b>Note</b> that during the benchmarks, a couple of temporary files are written
+(options
<tt>-b</tt>*), these will be automatically deleted after each test.<p>
If you want the simulation to be started automatically with the
optimized parameters, use the command line option <tt>-launch</tt>.<p>
<P>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html"> perf.out</a></tt> </TD><TD> Output </TD><TD> Generic output file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-err</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> errors.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-err</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">bencherr.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-so</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> tuned.tpr</a></tt> </TD><TD> Output </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dhdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-field</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> field.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-tabletf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tabletf.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tablep</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tablep.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tableb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpi.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tpid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpidist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html"> sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html"> sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> edsam.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-j</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html"> wham.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-jo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html"> bam.gct</a></tt> </TD><TD> Output, Opt. </TD><TD> General coupling stuff </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> gct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-runav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> runaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-px</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pullx.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-pf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pullf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ro</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rotation.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ra</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">rotangles.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">rotslabs.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">rottorque.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-mtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> nm.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> dipole.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> bench.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> bench.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-be</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html"> bench.edr</a></tt> </TD><TD> Output </TD><TD> Energy file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bg</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> bench.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-beo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html"> bench.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-beo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchedo.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bdhdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchdhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bfield</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchfld.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-btpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchtpi.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-brunav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchrnav.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bpx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> benchpx.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bpf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> benchpf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-bro</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">benchrot.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-bra</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">benchrota.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-brs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">benchrots.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-brt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">benchrott.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bmtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> benchn.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bdn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> bench.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of nodes to run the tests on (must be > 2 for separate PME nodes) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-npstring</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>-np</tt> </TD><TD> Specify the number of processors to $MPIRUN using this string: <tt>-np</tt>, <tt>-n</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nt</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of threads to run the tests on (turns MPI & mpirun off) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-npstring</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>-np</tt> </TD><TD> Specify the number of processors to <tt>$MPIRUN</tt> using this string: <tt>-np</tt>, <tt>-n</tt> or <tt>none</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ntmpi</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of MPI-threads to run the tests on (turns MPI & mpirun off) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> Repeat each test this often </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> Max fraction of PME nodes to test with </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.25 </tt> </TD><TD> Min fraction of PME nodes to test with </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-npme</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Benchmark all possible values for -npme or just the subset that is expected to perform well: <tt>auto</tt>, <tt>all</tt> or <tt>subset</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-upfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1.2 </tt> </TD><TD> Upper limit for rcoulomb scaling factor (Note that rcoulomb upscaling results in fourier grid downscaling) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-downfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Lower limit for rcoulomb scaling factor </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ntpr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of <a href="tpr.html">tpr</a> files to benchmark. Create these many files with scaling factors ranging from 1.0 to fac. If < 1, automatically choose the number of <a href="tpr.html">tpr</a> files to test </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-four</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Use this fourierspacing value instead of the grid found in the <a href="tpr.html">tpr</a> input file. (Spacing applies to a scaling factor of 1.0 if multiple <a href="tpr.html">tpr</a> files are written) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-steps</tt></b> </TD><TD ALIGN=RIGHT> step </TD><TD ALIGN=RIGHT> <tt>1000</tt> </TD><TD> Take timings for these many steps in the benchmark runs </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-resetstep</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Let dlb equilibrate these many steps before timings are taken (reset cycle counters after these many steps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-simsteps</tt></b> </TD><TD ALIGN=RIGHT> step </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> If non-negative, perform these many steps in the real run (overwrite nsteps from <a href="tpr.html">tpr</a>, add cpt steps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]launch</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Lauch the real simulation after optimization </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-deffnm</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Set the default filename for all file options at launch time </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ddorder</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>interleave</tt> </TD><TD> DD node order: <tt>interleave</tt>, <tt>pp_pme</tt> or <tt>cartesian</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ddcheck</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Check for all bonded interactions with DD </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rdd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rcon</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance for P-LINCS (nm), 0 is estimate </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dlb</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Dynamic load balancing (with DD): <tt>auto</tt>, <tt>no</tt> or <tt>yes</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dds</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.8 </tt> </TD><TD> Minimum allowed dlb scaling of the DD cell size </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-gcom</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Global communication frequency </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Write a compact <a href="log.html">log</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]seppot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write separate V and dVdl terms for each interaction type and node to the <a href="log.html">log</a> file(s) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-pforce</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Print all forces larger than this (kJ/mol nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]reprod</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Try to avoid optimizations that affect binary reproducibility </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-cpt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>15 </tt> </TD><TD> Checkpoint interval (minutes) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]cpnum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Keep and number checkpoint files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]append</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names (for launch only) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-maxh</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Terminate after 0.99 times this time (hours) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-multi</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Do multiple simulations in parallel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-replex</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Attempt replica exchange every # steps </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-reseed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Seed for replica exchange, -1 is generate a seed </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ionize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a simulation including the effect of an X-Ray bombardment on your system </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-npme</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Within -min and -max, benchmark all possible values for <tt>-npme</tt>, or just a reasonable subset. Auto neglects -min and -max and chooses reasonable values around a guess for npme derived from the .<a href="tpr.html">tpr</a>: <tt>auto</tt>, <tt>all</tt> or <tt>subset</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fix</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-2</tt> </TD><TD> If >= -1, do not vary the number of PME-only nodes, instead use this fixed value and only vary rcoulomb and the PME grid spacing. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> If >0, maximal rcoulomb for -ntpr>1 (rcoulomb upscaling results in fourier grid downscaling) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> If >0, minimal rcoulomb for -ntpr>1 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]scalevdw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Scale rvdw along with rcoulomb </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ntpr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of <tt>.<a href="tpr.html">tpr</a></tt> files to benchmark. Create this many files with different rcoulomb scaling factors depending on -rmin and -rmax. If < 1, automatically choose the number of <tt>.<a href="tpr.html">tpr</a></tt> files to test </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-steps</tt></b> </TD><TD ALIGN=RIGHT> step </TD><TD ALIGN=RIGHT> <tt>1000</tt> </TD><TD> Take timings for this many steps in the benchmark runs </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-resetstep</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-simsteps</tt></b> </TD><TD ALIGN=RIGHT> step </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> If non-negative, perform this many steps in the real run (overwrites nsteps from <tt>.<a href="tpr.html">tpr</a></tt>, add <tt>.cpt</tt> steps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]launch</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Launch the real simulation after optimization </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]bench</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Run the benchmarks or just create the input <tt>.<a href="tpr.html">tpr</a></tt> files? </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]append</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names (for launch only) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cpnum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Keep and number checkpoint files (launch only) </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_vanhove</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_vanhove computes the Van Hove correlation function.
-The Van Hove G(r,t) is the probability that a particle that is at r0
-at time zero can be found at position r0+r at time t.
-g_vanhove determines G not for a vector r, but for the length of r.
+<tt>g_vanhove</tt> computes the Van Hove correlation function.
+The Van Hove G(r,t) is the probability that a particle that is at r_0
+at time zero can be found at position r_0+r at time t.
+<tt>g_vanhove</tt> determines G not for a vector r, but for the length of r.
Thus it gives the probability that a particle moves a distance of r
in time t.
Jumps across the periodic boundaries are removed.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-sqrt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fm</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of frames in the matrix, 0 is plot all </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>2 </tt> </TD><TD> Maximum r in the matrix (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.01 </tt> </TD><TD> Binwidth in the matrix and for -or (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.01 </tt> </TD><TD> Binwidth in the matrix and for <tt>-or</tt> (nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-mmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum density in the matrix, 0 is calculate (1/nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>81</tt> </TD><TD> Number of levels in the matrix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of curves for the -or output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Frame spacing for the -or output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Integration limit for the -ot output (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ft</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of frames in the -ot output, 0 is plot all </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of curves for the <tt>-or</tt> output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Frame spacing for the <tt>-or</tt> output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Integration limit for the <tt>-ot</tt> output (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ft</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of frames in the <tt>-ot</tt> output, 0 is plot all </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_velacc</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_velacc computes the velocity autocorrelation function.
+<tt>g_velacc</tt> computes the velocity autocorrelation function.
When the <tt>-m</tt> option is used, the momentum autocorrelation
function is calculated.<p>
With option <tt>-mol</tt> the velocity autocorrelation function of
molecules is calculated. In this case the index group should consist
-of molecule numbers instead of atom numbers.
+of molecule numbers instead of atom numbers.<p>
+Be sure that your trajectory contains frames with velocity information
+(i.e. <tt>nstvout</tt> was set in your original <tt>.<a href="mdp.html">mdp</a></tt> file),
+and that the time interval between data collection points is
+much shorter than the time scale of the autocorrelation.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> vac.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-os</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">spectrum.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the momentum autocorrelation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the velocity acf of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the momentum autocorrelation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]recip</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use cm^-1 on X-axis instead of 1/ps for spectra. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the velocity acf of molecules </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
</TABLE>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_wham</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
This is an analysis program that implements the Weighted
Histogram Analysis Method (WHAM). It is intended to analyze
output files generated by umbrella sampling simulations to
-compute a potential of mean force (PMF). <p>
-At present, three input modes are supported:<br>
+compute a potential of mean force (PMF). <p>
+At present, three input modes are supported.<br>
<tt>*</tt> With option <tt>-it</tt>, the user provides a file which contains the
- filenames of the umbrella simulation run-input files (<a href="tpr.html">tpr</a> files),
- AND, with option -ix, a file which contains filenames of
- the pullx <a href="mdrun.html">mdrun</a> output files. The <a href="tpr.html">tpr</a> and pullx files must
- be in corresponding order, i.e. the first <a href="tpr.html">tpr</a> created the
- first pullx, etc.<br>
+ file names of the umbrella simulation run-input files (<tt>.<a href="tpr.html">tpr</a></tt> files),
+ AND, with option <tt>-ix</tt>, a file which contains file names of
+ the pullx <tt><a href="mdrun.html">mdrun</a></tt> output files. The <tt>.<a href="tpr.html">tpr</a></tt> and pullx files must
+ be in corresponding order, i.e. the first <tt>.<a href="tpr.html">tpr</a></tt> created the
+ first pullx, etc.<br>
<tt>*</tt> Same as the previous input mode, except that the the user
- provides the pull force ouput file names (pullf.<a href="xvg.html">xvg</a>) with option -if.
- From the pull force the position in the ubrella potential is
- computed. This does not work with tabulated umbrella potentials.
-<tt>*</tt> With option <tt>-ip</tt>, the user provides filenames of (gzipped) pdo files, i.e.
- the gromacs 3.3 umbrella output files. If you have some unusual
- reaction coordinate you may also generate your own pdo files and
- feed them with the -ip option into to g_wham. The pdo file header
- must be similar to the folowing:<br>
+ provides the pull force output file names (<tt>pullf.<a href="xvg.html">xvg</a></tt>) with option <tt>-if</tt>.
+ From the pull force the position in the umbrella potential is
+ computed. This does not work with tabulated umbrella potentials.<br><tt>*</tt> With option <tt>-ip</tt>, the user provides file names of (gzipped) <tt>.pdo</tt> files, i.e.
+ the GROMACS 3.3 umbrella output files. If you have some unusual reaction coordinate you may also generate your own <tt>.pdo</tt> files and
+ feed them with the <tt>-ip</tt> option into to <tt>g_wham</tt>. The <tt>.pdo</tt> file header
+ must be similar to the following:<p>
<tt># UMBRELLA 3.0<br>
# Component selection: 0 0 1<br>
# nSkip 1<br>
# Nr. of pull groups 2<br>
# Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0<br>
# Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0<br>
-#####</tt><br>
- Nr of pull groups, umbrella positions, force constants, and names
- may (of course) differ. Following the header, a time column and
- a data columns for each pull group follow (i.e. the displacement
- with respect to the umbrella center). Up to four pull groups are possible
+#####</tt><p>
+The number of pull groups, umbrella positions, force constants, and names
+may (of course) differ. Following the header, a time column and
+a data column for each pull group follows (i.e. the displacement
+with respect to the umbrella center). Up to four pull groups are possible
+
per <tt>.pdo</tt> file at present.<p>
By default, the output files are<br>
<tt>-o</tt> PMF output file<br>
- <tt>-hist</tt> histograms output file<p>
+ <tt>-hist</tt> Histograms output file<br>
+Always check whether the histograms sufficiently overlap.<p>
The umbrella potential is assumed to be harmonic and the force constants are
-read from the <a href="tpr.html">tpr</a> or pdo files. If a non-harmonic umbrella force was applied
-a tabulated potential can be provi
ed with -tab.<p>
-WHAM OPTIONS<p>
- <tt>-bins</tt> Nr of bins used in analysis<br>
+read from the <tt>.<a href="tpr.html">tpr</a></tt> or <tt>.pdo</tt> files. If a non-harmonic umbrella force was applied
+a tabulated potential can be provi
ded with <tt>-tab</tt>.<p>
+WHAM OPTIONS<br>------------<br>
+ <tt>-bins</tt> Number of bins used in analysis<br>
<tt>-temp</tt> Temperature in the simulations<br>
<tt>-tol</tt> Stop iteration if profile (probability) changed less than tolerance<br>
- <tt>-auto</tt> Automatic determination of boudndaries<br>
+ <tt>-auto</tt> Automatic determination of boundaries<br>
<tt>-min,-max</tt> Boundaries of the profile <br>
-The data points which are used
-to compute the profile can be restricted with options -b, -e, and -dt.
-Play particularly with -b to ensure sufficient equilibration in each
-umbrella window!<p>
-With -<a href="log.html">log</a> (default) the profile is written in energy units, otherwise (-nolog) as
-probability. The unit can be specified with -unit. With energy output,
-the energy in the first bin is defined to be zero. If you want the free energy at a different
-position to be zero, choose with -zprof0 (useful with bootstrapping, see below).<p>
-For cyclic (or periodic) reaction coordinates (dihedral angle, channel PMF
-without osmotic gradient), -cycl is useful.<br>
-<tt>-cycl yes</tt> min and max are assumed to
-be neighboring points and histogram points outside min and max are mapped into
-the interval [min,max] (compare histogram output). <br>
-<tt>-cycl weighted</tt> First, a non-cyclic profile is computed. Subsequently,
-periodicity is enforced by adding corrections dG(i) between neighboring bins
-i and i+1. The correction is chosen proportional to 1/[n(i)*n(i+1)]^alpha, where
-n(i) denotes the total nr of data points in bin i as collected from all histograms.
-alpha is defined with -alpha. The corrections are written to the file defined by -wcorr.
- (Compare Hub and de Groot, PNAS 105:1198 (2008))<p>
-ERROR ANALYSIS<br>
+The data points that are used to compute the profile
+can be restricted with options <tt>-b</tt>, <tt>-e</tt>, and <tt>-dt</tt>.
+Adjust <tt>-b</tt> to ensure sufficient equilibration in each
+umbrella window.<p>
+With <tt>-<a href="log.html">log</a></tt> (default) the profile is written in energy units, otherwise
+(with <tt>-nolog</tt>) as probability. The unit can be specified with <tt>-unit</tt>.
+With energy output, the energy in the first bin is defined to be zero.
+If you want the free energy at a different
+position to be zero, set <tt>-zprof0</tt> (useful with bootstrapping, see below).<p>
+For cyclic or periodic reaction coordinates (dihedral angle, channel PMF
+without osmotic gradient), the option <tt>-cycl</tt> is useful. <tt>g_wham</tt> will make use of the
+periodicity of the system and generate a periodic PMF. The first and the last bin of the
+reaction coordinate will assumed be be neighbors.<p>
+Option <tt>-sym</tt> symmetrizes the profile around z=0 before output,
+which may be useful for, e.g. membranes.<p>
+AUTOCORRELATIONS<br>----------------<br>
+With <tt>-ac</tt>, <tt>g_wham</tt> estimates the integrated autocorrelation
+time (IACT) τ for each umbrella window and weights the respective
+window with 1/[1+2*τ/dt]. The IACTs are written
+to the file defined with <tt>-oiact</tt>. In verbose mode, all
+autocorrelation functions (ACFs) are written to <tt>hist_autocorr.<a href="xvg.html">xvg</a></tt>.
+Because the IACTs can be severely underestimated in case of limited
+sampling, option <tt>-acsig</tt> allows one to smooth the IACTs along the
+reaction coordinate with a Gaussian (σ provided with <tt>-acsig</tt>,
+see output in <tt>iact.<a href="xvg.html">xvg</a></tt>). Note that the IACTs are estimated by simple
+integration of the ACFs while the ACFs are larger 0.05.
+If you prefer to compute the IACTs by a more sophisticated (but possibly
+less robust) method such as fitting to a double exponential, you can
+compute the IACTs with <tt><a href="g_analyze.html">g_analyze</a></tt> and provide them to <tt>g_wham</tt> with the file
+<tt>iact-in.<a href="dat.html">dat</a></tt> (option <tt>-iiact</tt>), which should contain one line per
+input file (<tt>.pdo</tt> or pullx/f file) and one column per pull group in the respective file.<p>
+ERROR ANALYSIS<br>--------------<br>
Statistical errors may be estimated with bootstrap analysis. Use it with care,
-otherwise the statistical error may be substantially undererstimated !!<br>
-<tt>-nBootstrap</tt> defines the nr of bootstraps. Two bootstrapping modes are supported.<br>
-<tt>-histbs</tt> Complete histograms are considered as independent data points (default). For each
-bootstrap, N histograms are randomly chosen from the N given histograms (allowing duplication).
-To avoid gaps without data along the reaction coordinate blocks of histograms (-histbs-block)
-may be defined. In that case, the given histograms are divided into blocks and
-only histograms within each block are mixed. Note that the histograms
-within each block must be representative for all possible histograms, otherwise the
-statistical error is undererstimated!<br>
-<tt>-nohistbs</tt> The given histograms are used to generate new random histograms,
-such that the generated data points are distributed according the given histograms. The number
-of points generated for each bootstrap histogram can be controlled with -bs-dt.
-Note that one data point should be generated for each *independent* point in the given
-histograms. With the long autocorrelations in MD simulations, this procedure may
-easily understimate the error!<br>
-Bootstrapping output:<br>
-<tt>-bsres</tt> Average profile and standard deviations<br>
-<tt>-bsprof</tt> All bootstrapping profiles<br>
-With <tt>-vbs</tt> (verbose bootstrapping), the histograms of each bootstrap are written, and,
-with <tt>-nohistBS</tt>, the cummulants of the histogram.
+otherwise the statistical error may be substantially underestimated.
+More background and examples for the bootstrap technique can be found in
+Hub, de Groot and Van der Spoel, JCTC (2010) 6: 3713-3720.<br>
+<tt>-nBootstrap</tt> defines the number of bootstraps (use, e.g., 100).
+Four bootstrapping methods are supported and
+selected with <tt>-bs-method</tt>.<br>
+ (1) <tt>b-hist</tt> Default: complete histograms are considered as independent
+data points, and the bootstrap is carried out by assigning random weights to the
+histograms ("Bayesian bootstrap"). Note that each point along the reaction coordinate
+must be covered by multiple independent histograms (e.g. 10 histograms), otherwise the
+statistical error is underestimated.<br>
+ (2) <tt>hist</tt> Complete histograms are considered as independent data points.
+For each bootstrap, N histograms are randomly chosen from the N given histograms
+(allowing duplication, i.e. sampling with replacement).
+To avoid gaps without data along the reaction coordinate blocks of histograms
+(<tt>-histbs-block</tt>) may be defined. In that case, the given histograms are
+divided into blocks and only histograms within each block are mixed. Note that
+the histograms within each block must be representative for all possible histograms,
+otherwise the statistical error is underestimated.<br>
+ (3) <tt>traj</tt> The given histograms are used to generate new random trajectories,
+such that the generated data points are distributed according the given histograms
+and properly autocorrelated. The autocorrelation time (ACT) for each window must be
+known, so use <tt>-ac</tt> or provide the ACT with <tt>-iiact</tt>. If the ACT of all
+windows are identical (and known), you can also provide them with <tt>-bs-tau</tt>.
+Note that this method may severely underestimate the error in case of limited sampling,
+that is if individual histograms do not represent the complete phase space at
+the respective positions.<br>
+ (4) <tt>traj-gauss</tt> The same as method <tt>traj</tt>, but the trajectories are
+not bootstrapped from the umbrella histograms but from Gaussians with the average
+and width of the umbrella histograms. That method yields similar error estimates
+like method <tt>traj</tt>.<p>Bootstrapping output:<br>
+ <tt>-bsres</tt> Average profile and standard deviations<br>
+ <tt>-bsprof</tt> All bootstrapping profiles<br>
+With <tt>-vbs</tt> (verbose bootstrapping), the histograms of each bootstrap are written,
+and, with bootstrap method <tt>traj</tt>, the cumulative distribution functions of
+the histograms.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TD ALIGN=RIGHT> <b><tt>-ip</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">pdo-files.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> profile.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-hist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> histo.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oiact</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> iact.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-iiact</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> iact-in.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bsres</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bsResult.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bsprof</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> bsProfs.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tab</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> umb-pot.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-wcorr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">cycl-corr.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum coordinate in profile </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum coordinate in profile </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]auto</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> determine min and max automatically </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]auto</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Determine min and max automatically </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bins</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>200</tt> </TD><TD> Number of bins in profile </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298 </tt> </TD><TD> Temperature </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1e-06 </tt> </TD><TD> Tolerance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> verbose mode </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>50 </tt> </TD><TD> first time to analyse (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1e+20 </tt> </TD><TD> last time to analyse (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Verbose mode </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>50 </tt> </TD><TD> First time to analyse (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1e+20 </tt> </TD><TD> Last time to analyse (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Analyse only every dt ps </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]histonly</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write histograms and exit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]boundsonly</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Determine min and max and exit (with -auto) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]log</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Calculate the <a href="log.html">log</a> of the profile before printing </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-unit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>kJ</tt> </TD><TD> energy unit in case of <a href="log.html">log</a> output: <tt>kJ</tt>, <tt>kCal</tt> or <tt>kT</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-zprof0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Define profile to 0.0 at this position (with -<a href="log.html">log</a>) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-cycl</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Create cyclic/periodic profile. Assumes min and max are the same point.: <tt>no</tt>, <tt>yes</tt> or <tt>weighted</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-alpha</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>2 </tt> </TD><TD> for '-cycl weighted', set parameter alpha </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]flip</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Combine halves of profile (not supported) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]hist-eq</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Enforce equal weight for all histograms. (Non-Weighed-HAM) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nBootstrap</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> nr of bootstraps to estimate statistical uncertainty </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bs-dt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> timestep for synthetic bootstrap histograms (ps). Ensure independent data points! </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bs-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> seed for bootstrapping. (-1 = use time) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]histbs</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> In bootstrapping, consider complete histograms as one data point. Accounts better for long autocorrelations. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-histbs-block</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>8</tt> </TD><TD> when mixin histograms only mix within blocks of -histBS_block. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vbs</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> verbose bootstrapping. Print the cummulants and a histogram file for each bootstrap. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]histonly</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write histograms and exit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]boundsonly</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Determine min and max and exit (with <tt>-auto</tt>) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]log</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Calculate the <a href="log.html">log</a> of the profile before printing </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-unit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>kJ</tt> </TD><TD> Energy unit in case of <a href="log.html">log</a> output: <tt>kJ</tt>, <tt>kCal</tt> or <tt>kT</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-zprof0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Define profile to 0.0 at this position (with <tt>-<a href="log.html">log</a></tt>) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cycl</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Create cyclic/periodic profile. Assumes min and max are the same point. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sym</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Symmetrize profile around z=0 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ac</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate integrated autocorrelation times and use in wham </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-acsig</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Smooth autocorrelation times along reaction coordinate with Gaussian of this σ </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ac-trestart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> When computing autocorrelation functions, restart computing every .. (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nBootstrap</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> nr of bootstraps to estimate statistical uncertainty (e.g., 200) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bs-method</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>b-hist</tt> </TD><TD> Bootstrap method: <tt>b-hist</tt>, <tt>hist</tt>, <tt>traj</tt> or <tt>traj-gauss</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bs-tau</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Autocorrelation time (ACT) assumed for all histograms. Use option <tt>-ac</tt> if ACT is unknown. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bs-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Seed for bootstrapping. (-1 = use time) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-histbs-block</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>8</tt> </TD><TD> When mixing histograms only mix within blocks of <tt>-histbs-block</tt>. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vbs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Verbose bootstrapping. Print the CDFs and a histogram file for each bootstrap. </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_wheel</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-<
a href="wheel.html">wheel</a> plots a helical <a href="wheel.html">wheel</a> representation of your sequence.
-The input sequence is in the .<a href="dat.html">dat</a> file where the first line contains
-the number of residues and each consecutive line contains a residuename.
+<
tt>g_<a href="wheel.html">wheel</a></tt> plots a helical <a href="wheel.html">wheel</a> representation of your sequence.
+The input sequence is in the <tt>.<a href="dat.html">dat</a></tt> file where the first line contains
+the number of residues and each consecutive line contains a residue name.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The first residue number in the sequence </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rot0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Rotate around an angle initially (90 degrees makes sense) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Plot a title in the center of the <a href="wheel.html">wheel</a> (must be shorter than 10 characters, or it will overwrite the <a href="wheel.html">wheel</a>) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nn</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Toggle numbers </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nn</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Toggle numbers </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_x2top</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-<a href="x2top.html">x2top</a> generates a primitive topology from a coordinate file.
+<tt>g_<a href="x2top.html">x2top</a></tt> generates a primitive topology from a coordinate file.
The program assumes all hydrogens are present when defining
the hybridization from the atom name and the number of bonds.
-The program can also make an <a href="rtp.html">rtp</a> entry, which you can then add
-to the <
a href="rtp.html">rtp</a> database.<p>
+The program can also make an <tt>.<a href="rtp.html">rtp</a></tt> entry, which you can then add
+to the <
tt>.<a href="rtp.html">rtp</a></tt> database.<p>
When <tt>-param</tt> is set, equilibrium distances and angles
and force constants will be printed in the topology for all
interactions. The equilibrium distances and angles are taken
G53a5 GROMOS96 53a5 Forcefield (official distribution)<p>
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<p>
The corresponding data files can be found in the library directory
-with name atomname2type.n2t. Check chapter 5 of the manual for more
-information about file formats. By default the forcefield selection
+with name <tt>atomname2type.n2t</tt>. Check Chapter 5 of the manual for more
+information about file formats. By default, the force field selection
is interactive, but you can use the <tt>-ff</tt> option to specify
one of the short names above on the command line instead. In that
-case <
a href="pdb2gmx.html">pdb2gmx</a> just looks for the corresponding file.<p>
+case <
tt>g_<a href="x2top.html">x2top</a></tt> just looks for the corresponding file.<p>
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ff</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>oplsaa</tt> </TD><TD> Force field for your simulation. Type "select" for interactive selection. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT>
gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate verbose output in the <a href="top.html">top</a> file. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate verbose output in the <a href="top.html">top</a> file. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nexcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of exclusions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use 3rd neighbour interactions for hydrogen atoms </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]alldih</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate all proper dihedrals </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]remdih</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove dihedrals on the same bond as an improper </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Output 1-4 interactions (pairs) in topology file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use 3rd neighbour interactions for hydrogen atoms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]alldih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate all proper dihedrals </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]remdih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove dihedrals on the same bond as an improper </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Output 1-4 interactions (pairs) in topology file </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-name</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>ICE</tt> </TD><TD> Name of your molecule </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pdbq</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the B-factor supplied in a <a href="pdb.html">pdb</a> file for the atomic charges </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]param</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print parameters in the output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Round off measured values </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pdbq</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the B-factor supplied in a <tt>.<a href="pdb.html">pdb</a></tt> file for the atomic charges </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]param</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print parameters in the output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Round off measured values </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-kb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400000</tt> </TD><TD> Bonded force constant (kJ/mol/nm^2) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-kt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400 </tt> </TD><TD> Angle force constant (kJ/mol/rad^2) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-kp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Dihedral angle force constant (kJ/mol/rad^2) </TD></TD>
<LI>The atom type selection is primitive. Virtually no chemical knowledge is used
<LI>Periodic boundary conditions screw up the bonding
<LI>No improper dihedrals are generated
-<LI>The atoms to atomtype translation table is incomplete (atomname2type.n2t files in the data directory). Please extend it and send the results back to the GROMACS crew.
+<LI>The atoms to atomtype translation table is incomplete (<tt>atomname2type.n2t</tt> file in the data directory). Please extend it and send the results back to the GROMACS crew.
</UL>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genbox</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-
Genbox can do one of 3 things:<p>
-1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and
-
-cp with a structure file with a box, but without atoms.<p>
-2) Solvate a solute configuration, eg. a protein, in a bath of solvent
+
<tt>genbox</tt> can do one of 3 things:<p>
+1) Generate a box of solvent. Specify <tt>-cs</tt> and <tt>-box</tt>. Or specify <tt>-cs</tt> and
+
<tt>-cp</tt> with a structure file with a box, but without atoms.<p>
+2) Solvate a solute configuration, e.g. a protein, in a bath of solvent
molecules. Specify <tt>-cp</tt> (solute) and <tt>-cs</tt> (solvent).
The box specified in the solute coordinate file (<tt>-cp</tt>) is used,
unless <tt>-box</tt> is set.
to change the box dimensions and center the solute.
Solvent molecules are removed from the box where the
distance between any atom of the solute molecule(s) and any atom of
-the solvent molecule is less than the sum of the VanderWaals radii of
-both atoms. A database (<tt>vdwradii.<a href="dat.html">dat</a></tt>) of VanderWaals radii is
-read by the program, atoms not in the database are
+the solvent molecule is less than the sum of the van der Waals radii of
+both atoms. A database (<tt>vdwradii.<a href="dat.html">dat</a></tt>) of van der Waals radii is
+read by the program, and atoms not in the database are
assigned a default distance <tt>-vdwd</tt>.
Note that this option will also influence the distances between
solvent molecules if they contain atoms that are not in the database.
at random positions.
The program iterates until <tt>nmol</tt> molecules
have been inserted in the box. To test whether an insertion is
-successful the same VanderWaals criterium is used as for removal of
-solvent molecules. When no appropriately
-sized holes (holes that can hold an extra molecule) are available the
+successful the same van der Waals criterium is used as for removal of
+solvent molecules. When no appropriately-sized
+holes (holes that can hold an extra molecule) are available, the
program tries for <tt>-nmol</tt> * <tt>-try</tt> times before giving up.
-Increase -try if you have several small holes to fill.<p>
+Increase <tt>-try</tt> if you have several small holes to fill.<p>
+If you need to do more than one of the above operations, it can be
+best to call <tt>genbox</tt> separately for each operation, so that
+you are sure of the order in which the operations occur.<p>
The default solvent is Simple Point Charge water (SPC), with coordinates
from <tt>$GMXLIB/spc216.<a href="gro.html">gro</a></tt>. These coordinates can also be used
for other 3-site water models, since a short equibilibration will remove
equlibrated in periodic boundary conditions to ensure a good
alignment of molecules on the stacking interfaces.
The <tt>-maxsol</tt> option simply adds only the first <tt>-maxsol</tt>
-solvent molecules and leaves out the rest would have fit into the box.
-<p>
+solvent molecules and leaves out the rest that would have fitted
+into the box. This can create a void that can cause problems later.
+Choose your volume wisely.<p>
The program can optionally rotate the solute molecule to align the
longest molecule axis along a box edge. This way the amount of solvent
molecules necessary is reduced.
It should be kept in mind that this only works for
-short simulations, as eg. an alpha-helical peptide in solution can
+short simulations, as e.g. an alpha-helical peptide in solution can
rotate over 90 degrees, within 500 ps. In general it is therefore
better to make a more or less cubic box.<p>
-Setting -shell larger than zero will place a layer of water of
+Setting <tt>-shell</tt> larger than zero will place a layer of water of
the specified thickness (nm) around the solute. Hint: it is a good
-idea to put the protein in the center of a box first (using <a href="editconf.html">editconf</a>).
+idea to put the protein in the center of a box first (using <tt><a href="editconf.html">editconf</a></tt>).
<p>
-Finally, genbox will optionally remove lines from your topology file in
+Finally, <tt>genbox</tt> will optionally remove lines from your topology file in
which a number of solvent molecules is already added, and adds a
line with the total number of solvent molecules in your coordinate file.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> box size </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> no of extra molecules to insert </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-try</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> try inserting -nmol*-try times </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1997</tt> </TD><TD> random generator seed </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-vdwd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.105 </tt> </TD><TD> default vdwaals distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> thickness of optional water layer around solute </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-maxsol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> keep velocities from input solute and solvent </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Box size </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of extra molecules to insert </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-try</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Try inserting <tt>-nmol</tt> times <tt>-try</tt> times </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1997</tt> </TD><TD> Random generator seed </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-vdwd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.105 </tt> </TD><TD> Default van der Waals distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Thickness of optional water layer around solute </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxsol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Keep velocities from input solute and solvent </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-genconf multiplies a given coordinate file by simply stacking them
+<tt>genconf</tt> multiplies a given coordinate file by simply stacking them
on <a href="top.html">top</a> of each other, like a small child playing with wooden blocks.
-The program makes a grid of <it>user defined</it>
+The program makes a grid of <it>user-defined</it>
proportions (<tt>-nbox</tt>),
and interspaces the grid point with an extra space <tt>-dist</tt>.<p>
When option <tt>-rot</tt> is used the program does not check for overlap
between molecules on grid points. It is recommended to make the box in
the input file at least as big as the coordinates +
-
Van der Waals radius.<p>
+
van der Waals radius.<p>
If the optional trajectory file is given, conformations are not
generated, but read from this file and translated appropriately to
build the grid.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nbox</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Number of boxes </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Distance between boxes </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Random generator seed, if 0 generated from the time </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Randomly rotate conformations </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]shuffle</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Random shuffling of molecules </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sort molecules on X coord </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Randomly rotate conformations </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]shuffle</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Random shuffling of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sort molecules on X coord </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-block</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Divide the box in blocks on this number of cpus </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nmolat</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system! </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-maxrot</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>180 180 180</tt> </TD><TD> Maximum random rotation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]renumber</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Renumber residues </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]renumber</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Renumber residues </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genion</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-genion replaces solvent molecules by monoatomic ions at
+<tt>genion</tt> replaces solvent molecules by monoatomic ions at
the position of the first atoms with the most favorable electrostatic
potential or at random. The potential is calculated on all atoms, using
-normal GROMACS particle based methods (in contrast to other methods
+normal GROMACS particle-based methods (in contrast to other methods
based on solving the Poisson-Boltzmann equation).
The potential is recalculated after every ion insertion.
If specified in the run input file, a reaction field, shift function
The user should add the ion molecules to the topology file or use
the <tt>-p</tt> option to automatically modify the topology.<p>
The ion molecule type, residue and atom names in all force fields
-are the capitalized element names without sign. Ions which can have
-multiple charge states get the multiplicilty added, without sign,
-for the uncommon states only.<p>
+are the capitalized element names without sign. This molecule name
+should be given with <tt>-pname</tt> or <tt>-nname</tt>, and the
+<tt>[molecules]</tt> section of your topology updated accordingly,
+either by hand or with <tt>-p</tt>. Do not use an atom name instead!
+<p>Ions which can have multiple charge states get the multiplicity
+added, without sign, for the uncommon states only.<p>
With the option <tt>-pot</tt> the potential can be written as B-factors
-in a <a href="pdb.html">pdb</a> file (for visualisation using e.g. rasmol).
+in a <tt>.<a href="pdb.html">pdb</a></tt> file (for visualisation using e.g. Rasmol).
The unit of the potential is 1000 kJ/(mol e), the scaling be changed
with the <tt>-scale</tt> option.<p>
-For larger ions, e.g. sulfate we recommended to use <a href="genbox.html">genbox</a>.
+For larger ions, e.g. sulfate we recommended using <tt><a href="genbox.html">genbox</a></tt>.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of positive ions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>CL</tt> </TD><TD> Name of the negative ion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Charge of the negative ion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.6 </tt> </TD><TD> Minimum distance between ions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]random</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use random placement of ions instead of based on potential. The rmin option should still work </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]random</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use random placement of ions instead of based on potential. The rmin option should still work </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1993</tt> </TD><TD> Seed for random number generator </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Scaling factor for the potential for -pot </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-conc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input <a href="tpr.html">tpr</a> file. Overrides the -np and nn options. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]neutral</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Scaling factor for the potential for <tt>-pot</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-conc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input <tt>.<a href="tpr.html">tpr</a></tt> file. Overrides the <tt>-np</tt> and <tt>-nn</tt> options. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]neutral</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. </TD></TD>
</TABLE>
<P>
<H3>Known problems</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genpr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genrestr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-genrestr produces an include file for a topology containing
+<tt>genrestr</tt> produces an include file for a topology containing
a list of atom numbers and three force constants for the
-X, Y and Z direction. A single isotropic force constant may
+<it>x</it>-, <it>y</it>-, and <it>z</it>-direction. A single isotropic force constant may
be given on the command line instead of three components.<p>
WARNING: position restraints only work for the one molecule at a time.
Position restraints are interactions within molecules, therefore
they should be included within the correct <tt>[ moleculetype ]</tt>
block in the topology. Since the atom numbers in every moleculetype
in the topology start at 1 and the numbers in the input file for
-<a href="genpr.html">genpr</a> number consecutively from 1, <a href="genpr.html">genpr</a> will only produce a useful
-file for the first molecule.<p>
-The -of option produces an index file that can be used for
-freezing atoms. In this case
the input file must be a <a href="pdb.html">pdb</a> file.<p>
-With the <tt>-disre</tt> option half a matrix of distance restraints
+<tt>genrestr</tt> number consecutively from 1, <tt>genrestr</tt> will only
+
produce a useful file for the first molecule.<p>
+The <tt>-of</tt> option produces an index file that can be used for
+freezing atoms. In this case
, the input file must be a <tt>.<a href="pdb.html">pdb</a></tt> file.<p>
+With the <tt>-disre</tt> option, half a matrix of distance restraints
is generated instead of position restraints. With this matrix, that
-one typically would apply to C-alpha atoms in a protein, one can
+one typically would apply to Cα atoms in a protein, one can
maintain the overall conformation of a protein without tieing it to
a specific position (as with position restraints).
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fc</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1000 1000 1000</tt> </TD><TD> force constants (kJ mol-1 nm-2) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-freeze</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> if the -of option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]disre</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate a distance restraint matrix for all the atoms in index </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fc</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1000 1000 1000</tt> </TD><TD> Force constants (kJ/mol nm^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-freeze</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> If the <tt>-of</tt> option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]disre</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate a distance restraint matrix for all the atoms in index </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-disre_dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Distance range around the actual distance for generating distance restraints </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-disre_frac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-disre_up2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Only generate distance restraints for atoms pairs within cutoff (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]constr</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]constr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions. </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Contents</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxcheck</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-
gmxcheck reads a trajectory (<tt>.<a href="trj.html">trj</a></tt>, <tt>.<a href="trr.html">trr</a></tt> or
+
<tt>gmxcheck</tt> reads a trajectory (<tt>.<a href="trj.html">trj</a></tt>, <tt>.<a href="trr.html">trr</a></tt> or
<tt>.<a href="xtc.html">xtc</a></tt>), an energy file (<tt>.<a href="ene.html">ene</a></tt> or <tt>.<a href="edr.html">edr</a></tt>)
or an index file (<tt>.<a href="ndx.html">ndx</a></tt>)
and prints out useful information about them.<p>
no problem). If velocities are present, an estimated temperature
will be calculated from them.<p>
If an index file, is given its contents will be summarized.<p>
-If both a trajectory and a <a href="tpr.html">tpr</a> file are given (with <tt>-s1</tt>)
+If both a trajectory and a <tt>.<a href="tpr.html">tpr</a></tt> file are given (with <tt>-s1</tt>)
the program will check whether the bond lengths defined in the <a href="tpr.html">tpr</a>
file are indeed correct in the trajectory. If not you may have
non-matching files due to e.g. deshuffling or due to problems with
-virtual sites. With these flags,
gmxcheck provides a quick check for such problems.<p>
+virtual sites. With these flags,
<tt>gmxcheck</tt> provides a quick check for such problems.<p>
The program can compare two run input (<tt>.<a href="tpr.html">tpr</a></tt>, <tt>.<a href="tpb.html">tpb</a></tt> or
<tt>.<a href="tpa.html">tpa</a></tt>) files
when both <tt>-s1</tt> and <tt>-s2</tt> are supplied.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-vdwfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.8 </tt> </TD><TD> Fraction of sum of VdW radii used as warning cutoff </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bonlo</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.4 </tt> </TD><TD> Min. fract. of sum of VdW radii for bonded atoms </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-bonhi</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.7 </tt> </TD><TD> Max. fract. of sum of VdW radii for bonded atoms </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmsd</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print RMSD for x, v and f </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmsd</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print RMSD for x, v and f </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-abstol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Absolute tolerance, useful when sums are close to zero. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ab</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compare the A and B topology from one file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ab</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compare the A and B topology from one file </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-lastener</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. </TD></TD>
</TABLE>
<P>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Gmxdemo</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<P><H2>The GROMACS demo</A></H2>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxdump</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-
gmxdump reads a run input file (<tt>.<a href="tpa.html">tpa</a></tt>/<tt>.<a href="tpr.html">tpr</a></tt>/<tt>.<a href="tpb.html">tpb</a></tt>),
+
<tt>gmxdump</tt> reads a run input file (<tt>.<a href="tpa.html">tpa</a></tt>/<tt>.<a href="tpr.html">tpr</a></tt>/<tt>.<a href="tpb.html">tpb</a></tt>),
a trajectory (<tt>.<a href="trj.html">trj</a></tt>/<tt>.<a href="trr.html">trr</a></tt>/<tt>.<a href="xtc.html">xtc</a></tt>), an energy
file (<tt>.<a href="ene.html">ene</a></tt>/<tt>.<a href="edr.html">edr</a></tt>), or a checkpoint file (<tt>.cpt</tt>)
and prints that to standard output in a readable format.
This program is essential for checking your run input file in case of
problems.<p>
The program can also preprocess a topology to help finding problems.
-Note that currently setting GMXLIB is the only way to customize
+Note that currently setting <tt>GMXLIB</tt> is the only way to customize
directories used for searching include files.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nr</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sys</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> List the atoms and bonded interactions for the whole system instead of for each molecule type </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sys</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> List the atoms and bonded interactions for the whole system instead of for each molecule type </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
+<UL>
+<LI>Position restraint output from -sys -s is broken
+</UL>
+<P>
<hr>
<div ALIGN=RIGHT>
<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<p>Files with the gro file extension contain a molecular structure in
Gromos87 format. gro files can be used as trajectory by simply
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>grompp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
for hydrogens and heavy atoms.
Then a coordinate file is read and velocities can be generated
from a Maxwellian distribution if requested.
-grompp also reads parameters for the <a href="mdrun.html">mdrun</a>
+<tt>grompp</tt> also reads parameters for the <tt><a href="mdrun.html">mdrun</a></tt>
(eg. number of MD steps, time step, cut-off), and others such as
NEMD parameters, which are corrected so that the net acceleration
is zero.
Eventually a binary file is produced that can serve as the sole input
file for the MD program.<p>
-grompp uses the atom names from the topology file. The atom names
+<tt>grompp</tt> uses the atom names from the topology file. The atom names
in the coordinate file (option <tt>-c</tt>) are only read to generate
warnings when they do not match the atom names in the topology.
Note that the atom names are irrelevant for the simulation as
only the atom types are used for generating interaction parameters.<p>
-grompp uses a built-in preprocessor to resolve includes, macros
-etcetera. The preprocessor supports the following keywords:<br>
+<tt>grompp</tt> uses a built-in preprocessor to resolve includes, macros,
+etc. The preprocessor supports the following keywords:<p>
#ifdef VARIABLE<br>
#ifndef VARIABLE<br>
#else<br>
#endif<br>
#define VARIABLE<br>
#undef VARIABLE<br>#include "filename"<br>
-#include <filename><br>
+#include <filename><p>
The functioning of these statements in your topology may be modulated by
-using the following two flags in your <tt><a href="mdp.html">mdp</a></tt> file:<br>
-define = -DVARIABLE1 -DVARIABLE2<br>
-include = /home/john/doe<br>
+using the following two flags in your <tt>.<a href="mdp.html">mdp</a></tt> file:<p>
+<tt>define = -DVARIABLE1 -DVARIABLE2<br>
+include = -I/home/john/doe</tt><br>
For further information a C-programming textbook may help you out.
Specifying the <tt>-pp</tt> flag will get the pre-processed
topology file written out so that you can verify its contents.<p>
-If your system does not have a c-preprocessor, you can still
-use grompp, but you do not have access to the features
-from the cpp. Command line options to the c-preprocessor can be given
-in the <tt>.<a href="mdp.html">mdp</a></tt> file. See your local manual (man cpp).<p>
When using position restraints a file with restraint coordinates
can be supplied with <tt>-r</tt>, otherwise restraining will be done
with respect to the conformation from the <tt>-c</tt> option.
those of the A topology.<p>
Starting coordinates can be read from trajectory with <tt>-t</tt>.
The last frame with coordinates and velocities will be read,
-unless the <tt>-time</tt> option is used.
+unless the <tt>-time</tt> option is used. Only if this information
+is absent will the coordinates in the <tt>-c</tt> file be used.
Note that these velocities will not be used when <tt>gen_vel = yes</tt>
in your <tt>.<a href="mdp.html">mdp</a></tt> file. An energy file can be supplied with
<tt>-e</tt> to read Nose-Hoover and/or Parrinello-Rahman coupling
-variables. Note that for continuation it is better and easier to supply
-a checkpoint file directly to <a href="mdrun.html">mdrun</a>, since that always contains
-the complete state of the system and you don't need to generate
-a new run input file. Note that if you only want to change the number
-of run steps <a href="tpbconv.html">tpbconv</a> is more convenient than grompp.<p>
-Using the <tt>-morse</tt> option grompp can convert the harmonic bonds
-in your topology to morse potentials. This makes it possible to break
-bonds. For this option to work you need an extra file in your $GMXLIB
-with dissociation energy. Use the -debug option to get more information
-on the workings of this option (look for MORSE in the grompp.<a href="log.html">log</a> file
-using less or something like that).<p>
-By default all bonded interactions which have constant energy due to
+variables.<p>
+<tt>grompp</tt> can be used to restart simulations (preserving
+continuity) by supplying just a checkpoint file with <tt>-t</tt>.
+However, for simply changing the number of run steps to extend
+a run, using <tt><a href="tpbconv.html">tpbconv</a></tt> is more convenient than <tt>grompp</tt>.
+You then supply the old checkpoint file directly to <tt><a href="mdrun.html">mdrun</a></tt>
+with <tt>-cpi</tt>. If you wish to change the ensemble or things
+like output frequency, then supplying the checkpoint file to
+<tt>grompp</tt> with <tt>-t</tt> along with a new <tt>.<a href="mdp.html">mdp</a></tt> file
+with <tt>-f</tt> is the recommended procedure.<p>
+By default, all bonded interactions which have constant energy due to
virtual site constructions will be removed. If this constant energy is
not zero, this will result in a shift in the total energy. All bonded
interactions can be kept by turning off <tt>-rmvsbds</tt>. Additionally,
all constraints for distances which will be constant anyway because
of virtual site constructions will be removed. If any constraints remain
-which involve virtual sites, a fatal error will result.<p>To verify your run input file, please make notice of all warnings
+which involve virtual sites, a fatal error will result.<p>To verify your run input file, please take note of all warnings
on the screen, and correct where necessary. Do also look at the contents
-of the <tt>mdout.<a href="mdp.html">mdp</a></tt> file, this contains comment lines, as well as
-the input that <tt>grompp</tt> has read. If in doubt you can start grompp
+of the <tt>mdout.<a href="mdp.html">mdp</a></tt> file; this contains comment lines, as well as
+the input that <tt>grompp</tt> has read. If in doubt, you can start <tt>grompp</tt>
with the <tt>-debug</tt> option which will give you more information
-in a file called grompp.<a href="log.html">log</a> (along with real debug info). Finally, you
+in a file called <tt>grompp.<a href="log.html">log</a></tt> (along with real debug info). You
can see the contents of the run input file with the <tt><a href="gmxdump.html">gmxdump</a></tt>
-program.
+program. <tt><a href="gmxcheck.html">gmxcheck</a></tt> can be used to compare the contents of two
+run input files.<p>The <tt>-maxwarn</tt> option can be used to override warnings printed
+by <tt>grompp</tt> that otherwise halt output. In some cases, warnings are
+harmless, but usually they are not. The user is advised to carefully
+interpret the output messages before attempting to bypass them with
+this option.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html"> grompp.mdp</a></tt> </TD><TD> Input, Opt. </TD><TD> grompp input file with MD parameters </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html"> grompp.mdp</a></tt> </TD><TD> Input </TD><TD> grompp input file with MD parameters </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html"> mdout.mdp</a></tt> </TD><TD> Output </TD><TD> grompp input file with MD parameters </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Output </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Energy file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ref</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rotref.trr</a></tt> </TD><TD> In/Out, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Take frame at or first after this time. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmvsbds</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Remove constant bonded interactions with virtual sites </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-maxwarn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of allowed warnings during input processing </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]zero</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set parameters for bonded interactions without defaults to zero instead of generating an error </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]renum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Renumber atomtypes and minimize number of atomtypes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmvsbds</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Remove constant bonded interactions with virtual sites </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxwarn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of allowed warnings during input processing. Not for normal use and may generate unstable systems </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]zero</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set parameters for bonded interactions without defaults to zero instead of generating an error </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]renum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Renumber atomtypes and minimize number of atomtypes </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Files with the hat file extension contain
a fourier transform of a spread function used in the PPPM algorithm.
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>highway</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The itp file extension stands for include toplogy. These files are included in topology files ( with the <a href="top.html"><tt>top</tt></a> extension )
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Logfiles are generated by some GROMACS programs and are usually in
human-readable format. Use <tt>more logfile</tt>.
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The m2p file format contains input options for the
<a href="xpm2ps.html">xpm2ps</a> program. All of these options
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>make_edi</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-<tt>make_<a href="edi.html">edi</a></tt> generates an essential dynamics (ED) sampling input file to be used with <a href="mdrun.html">mdrun</a>
+<tt>make_<a href="edi.html">edi</a></tt> generates an essential dynamics (ED) sampling input file to be used with <tt><a href="mdrun.html">mdrun</a></tt>
based on eigenvectors of a covariance matrix (<tt><a href="g_covar.html">g_covar</a></tt>) or from a
-normal modes anaysis (<tt><a href="g_nmeig.html">g_nmeig</a></tt>).
+normal modes ana
lysis (<tt><a href="g_nmeig.html">g_nmeig</a></tt>).
ED sampling can be used to manipulate the position along collective coordinates
(eigenvectors) of (biological) macromolecules during a simulation. Particularly,
it may be used to enhance the sampling efficiency of MD simulations by stimulating
J. Biomol. Struct. Dyn. 13 : 741-751 (1996)<br>
B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen;
An extended sampling of the configurational space of HPr from E. coli
-PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996)
+Proteins: Struct. Funct. Gen. 26: 314-322 (1996)
<p>You will be prompted for one or more index groups that correspond to the eigenvectors,
reference structure, target positions, etc.<p>
<tt>-mon</tt>: monitor projections of the coordinates onto selected eigenvectors.<p>
<tt>-radfix</tt>: perform fixed-step radius expansion along selected eigenvectors.<p>
<tt>-radacc</tt>: perform acceptance radius expansion along selected eigenvectors.
(steps in the desired direction will be accepted, others will be rejected).
-Note: by default the starting MD structure will be taken as origin of the first
+<b>Note:</b> by default the starting MD structure will be taken as origin of the first
expansion cycle for radius expansion. If <tt>-ori</tt> is specified, you will be able
to read in a structure file that defines an external origin.<p>
<tt>-radcon</tt>: perform acceptance radius contraction along selected eigenvectors
towards a target structure specified with <tt>-tar</tt>.<p>
NOTE: each eigenvector can be selected only once. <p>
-<tt>-outfrq</tt>: frequency (in steps) of writing out projections etc. to
.<a href="edo.html">edo</a> file<p>
+<tt>-outfrq</tt>: frequency (in steps) of writing out projections etc. to
<tt>.<a href="xvg.html">xvg</a></tt> file<p>
<tt>-slope</tt>: minimal slope in acceptance radius expansion. A new expansion
cycle will be started if the spontaneous increase of the radius (in nm/step)
is less than the value specified.<p>
before a new cycle is started.<p>
Note on the parallel implementation: since ED sampling is a 'global' thing
(collective coordinates etc.), at least on the 'protein' side, ED sampling
-is not very parallel-friendly from an implentation point of view. Because
-parallel ED requires much extra communication, expect the performance to be
-lower as in a free MD simulation, especially on a large number of nodes. <p>
-All output of <a href="mdrun.html">mdrun</a> (specify with -eo) is written to a .<a href="edo.html">edo</a> file. In the output
-file, per OUTFRQ step the following information is present: <p>
-* the step number<br>
-* the number of the ED dataset. (Note that you can impose multiple ED constraints in
-a single simulation - on different molecules e.g. - if several .<a href="edi.html">edi</a> files were concatenated
-first. The constraints are applied in the order they appear in the .<a href="edi.html">edi</a> file.) <br>
-* RMSD (for atoms involved in fitting prior to calculating the ED constraints)<br>
-* projections of the positions onto selected eigenvectors<br>
+is not very parallel-friendly from an implementation point of view. Because
+parallel ED requires some extra communication, expect the performance to be
+lower as in a free MD simulation, especially on a large number of nodes and/or
+when the ED group contains a lot of atoms. <p>
+Please also note that if your ED group contains more than a single protein,
+then the <tt>.<a href="tpr.html">tpr</a></tt> file must contain the correct PBC representation of the ED group.
+Take a look on the initial RMSD from the reference structure, which is printed
+out at the start of the simulation; if this is much higher than expected, one
+of the ED molecules might be shifted by a box vector. <p>
+All ED-related output of <tt><a href="mdrun.html">mdrun</a></tt> (specify with <tt>-eo</tt>) is written to a <tt>.<a href="xvg.html">xvg</a></tt> file
+as a function of time in intervals of OUTFRQ steps.<p>
+<b>Note</b> that you can impose multiple ED constraints and flooding potentials in
+a single simulation (on different molecules) if several <tt>.<a href="edi.html">edi</a></tt> files were concatenated
+first. The constraints are applied in the order they appear in the <tt>.<a href="edi.html">edi</a></tt> file.
+Depending on what was specified in the <tt>.<a href="edi.html">edi</a></tt> input file, the output file contains for each ED dataset<p>
+<tt>*</tt> the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)<br>
+<tt>*</tt> projections of the positions onto selected eigenvectors<br>
<p><p>
FLOODING:<p>
-with -flood you can specify which eigenvectors are used to compute a flooding potential,
+with <tt>-flood</tt>, you can specify which eigenvectors are used to compute a flooding potential,
which will lead to extra forces expelling the structure out of the region described
by the covariance matrix. If you switch -restrain the potential is inverted and the structure
is kept in that region.
<p>
-The origin is normally the average structure stored in the eigvec.<a href="trr.html">trr</a> file.
-It can be changed with -ori to an arbitrary position in configurational space.
-With -tau, -deltaF0 and -Eflnull you control the flooding behaviour.
+The origin is normally the average structure stored in the <tt>eigvec.<a href="trr.html">trr</a></tt> file.
+It can be changed with <tt>-ori</tt> to an arbitrary position in configuration space.
+With <tt>-tau</tt>, <tt>-deltaF0</tt>, and <tt>-Eflnull</tt> you control the flooding behaviour.
Efl is the flooding strength, it is updated according to the rule of adaptive flooding.
-Tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth).
+Tau is the time constant of adaptive flooding, high τ means slow adaption (i.e. growth).
DeltaF0 is the flooding strength you want to reach after tau ps of simulation.
-To use constant Efl set -tau to zero.
+To use constant Efl set <tt>-tau</tt> to zero.
<p>
--alpha is a fudge parameter to control the width of the flooding potential. A value of 2 has been found
+<tt>-alpha</tt> is a fudge parameter to control the width of the flooding potential. A value of 2 has been found
to give good results for most standard cases in flooding of proteins.
-Alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
-increase, this is mimicked by alpha>1.
-For restraining alpha<1 can give you smaller width in the restraining potential.
+α basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
+increase, this is mimicked by α > 1.
+For restraining, α < 1 can give you smaller width in the restraining potential.
<p>
RESTART and FLOODING:
If you want to restart a crashed flooding simulation please find the values deltaF and Efl in
-the output file and manually put them into the .<a href="edi.html">edi</a> file under DELTA_F0 and EFL_NULL.
+the output file and manually put them into the <tt>.<a href="edi.html">edi</a></tt> file under DELTA_F0 and EFL_NULL.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-mon</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91 </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-linfix</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for fixed increment linear sampling </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-linacc</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for acceptance linear sampling </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-flood</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for flooding </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-radfix</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for fixed increment radius expansion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-radacc</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for acceptance radius expansion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-radcon</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for acceptance radius contraction </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-outfrq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Freqency (in steps) of writing output in .<a href="edo.html">edo</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-flood</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for flooding </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-outfrq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Freqency (in steps) of writing output in <tt>.<a href="xvg.html">xvg</a></tt> file </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-slope</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimal slope in acceptance radius expansion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-maxedsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Max nr of steps per cycle </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-deltaF0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>150 </tt> </TD><TD> Target destabilization energy - used for flooding </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-deltaF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Start deltaF with this parameter - default 0, i.e. nonzero values only needed for restart </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tau</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eqsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of steps to run without any perturbations </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-Eflnull</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> This is the starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. To use a constant flooding strength use -tau 0. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> T is temperature, the value is needed if you want to do flooding </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-alpha</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Scale width of gaussian flooding potential with alpha^2 </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-linstep</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! "1.0 2.3 5.1 -3.1") </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-accdir</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Directions for acceptance linear sampling - only sign counts! (put in quotes! "-1 +1 -1.1") </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-radstep</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Stepsize (nm/step) for fixed increment radius expansion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]restrain</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]hessian</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> The eigenvectors and eigenvalues are from a Hessian matrix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]harmonic</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> The eigenvalues are interpreted as spring constant </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxedsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Maximum number of steps per cycle </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eqsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of steps to run without any perturbations </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-deltaF0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>150 </tt> </TD><TD> Target destabilization energy for flooding </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-deltaF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Start deltaF with this parameter - default 0, nonzero values only needed for restart </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tau</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Eflnull</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> The starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. For a constant flooding strength use <tt>-tau</tt> 0. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> T is temperature, the value is needed if you want to do flooding </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-alpha</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Scale width of gaussian flooding potential with alpha^2 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]restrain</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]hessian</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> The eigenvectors and eigenvalues are from a Hessian matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]harmonic</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> The eigenvalues are interpreted as spring constant </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-constF</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Constant force flooding: manually set the forces for the eigenvectors selected with -flood (put in quotes! "1.0 2.3 5.1 -3.1"). No other flooding parameters are needed when specifying the forces directly. </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>make_ndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
Index groups are necessary for almost every gromacs program.
All these programs can generate default index groups. You ONLY
-have to use make_<a href="ndx.html">ndx</a> when you need SPECIAL index groups.
+have to use <tt>make_<a href="ndx.html">ndx</a></tt> when you need SPECIAL index groups.
There is a default index group for the whole system, 9 default
-index groups are generated for proteins, a default index group
+index groups for proteins, and a default index group
is generated for every other residue name.<p>
-When no index file is supplied, also make_<a href="ndx.html">ndx</a> will generate the
+When no index file is supplied, also <tt>make_<a href="ndx.html">ndx</a></tt> will generate the
default groups.
With the index editor you can select on atom, residue and chain names
and numbers.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-natoms</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> set number of atoms (default: read from coordinate or index file) </TD></TD>
</TABLE>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
This file maps matrix data to RGB values which is used by the
<a href="do_dssp.html">do_dssp</a> program.<p>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<P> Follow <a href="mdp_opt.html">this link</a> for a detailed description of the options</a>. </P>
<P> Below is a sample mdp file.
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdp options</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p> </p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p> </p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<!--
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-The mdrun program is the main computational chemistry engine
+The <tt>mdrun</tt> program is the main computational chemistry engine
within GROMACS. Obviously, it performs Molecular Dynamics simulations,
but it can also perform Stochastic Dynamics, Energy Minimization,
test particle insertion or (re)calculation of energies.
-Normal mode analysis is another option. In this case mdrun
+Normal mode analysis is another option. In this case <tt>mdrun</tt>
builds a Hessian matrix from single conformation.
For usual Normal Modes-like calculations, make sure that
the structure provided is properly energy-minimized.
-The generated matrix can be diagonalized by <
a href="g_nmeig.html">g_nmeig</a>.<p>
-The mdrun program reads the run input file (<tt>-s</tt>)
+The generated matrix can be diagonalized by <
tt><a href="g_nmeig.html">g_nmeig</a></tt>.<p>
+The <tt>mdrun</tt> program reads the run input file (<tt>-s</tt>)
and distributes the topology over nodes if needed.
-mdrun produces at least four output files.
+<tt>mdrun</tt> produces at least four output files.
A single <a href="log.html">log</a> file (<tt>-g</tt>) is written, unless the option
<tt>-seppot</tt> is used, in which case each node writes a <a href="log.html">log</a> file.
The trajectory file (<tt>-o</tt>), contains coordinates, velocities and
(<tt>-x</tt>).<p>
The option <tt>-dhdl</tt> is only used when free energy calculation is
turned on.<p>
-When mdrun is started using MPI with more than 1 node, parallelization
-is used. By default domain decomposition is used, unless the <tt>-pd</tt>
-option is set, which selects particle decomposition.<p>
+A simulation can be run in parallel using two different parallelization
+schemes: MPI parallelization and/or OpenMP thread parallelization.
+The MPI parallelization uses multiple processes when <tt>mdrun</tt> is
+compiled with a normal MPI library or threads when <tt>mdrun</tt> is
+compiled with the GROMACS built-in thread-MPI library. OpenMP threads
+are supported when mdrun is compiled with OpenMP. Full OpenMP support
+is only available with the Verlet cut-off scheme, with the (older)
+group scheme only PME-only processes can use OpenMP parallelization.
+In all cases <tt>mdrun</tt> will by default try to use all the available
+hardware resources. With a normal MPI library only the options
+<tt>-ntomp</tt> (with the Verlet cut-off scheme) and <tt>-ntomp_pme</tt>,
+for PME-only processes, can be used to control the number of threads.
+With thread-MPI there are additional options <tt>-nt</tt>, which sets
+the total number of threads, and <tt>-ntmpi</tt>, which sets the number
+of thread-MPI threads.
+Note that using combined MPI+OpenMP parallelization is almost always
+slower than single parallelization, except at the scaling limit, where
+especially OpenMP parallelization of PME reduces the communication cost.
+OpenMP-only parallelization is much faster than MPI-only parallelization
+on a single CPU(-die). Since we currently don't have proper hardware
+topology detection, <tt>mdrun</tt> compiled with thread-MPI will only
+automatically use OpenMP-only parallelization when you use up to 4
+threads, up to 12 threads with Intel Nehalem/Westmere, or up to 16
+threads with Intel Sandy Bridge or newer CPUs. Otherwise MPI-only
+parallelization is used (except with GPUs, see below).
+<p>
+To quickly test the performance of the new Verlet cut-off scheme
+with old <tt>.<a href="tpr.html">tpr</a></tt> files, either on CPUs or CPUs+GPUs, you can use
+the <tt>-testverlet</tt> option. This should not be used for production,
+since it can slightly modify potentials and it will remove charge groups
+making analysis difficult, as the <tt>.<a href="tpr.html">tpr</a></tt> file will still contain
+charge groups. For production simulations it is highly recommended
+to specify <tt>cutoff-scheme = Verlet</tt> in the <tt>.<a href="mdp.html">mdp</a></tt> file.
+<p>
+With GPUs (only supported with the Verlet cut-off scheme), the number
+of GPUs should match the number of MPI processes or MPI threads,
+excluding PME-only processes/threads. With thread-MPI the number
+of MPI threads will automatically be set to the number of GPUs detected.
+When you want to use a subset of the available GPUs, you can use
+the <tt>-gpu_id</tt> option, where GPU id's are passed as a string,
+e.g. 02 for using GPUs 0 and 2. When you want different GPU id's
+on different nodes of a compute cluster, use the GMX_GPU_ID environment
+variable instead. The format for GMX_GPU_ID is identical to
+<tt>-gpu_id</tt>, but an environment variable can have different values
+on different nodes of a cluster.
+<p>
+When using PME with separate PME nodes or with a GPU, the two major
+compute tasks, the non-bonded force calculation and the PME calculation
+run on different compute resources. If this load is not balanced,
+some of the resources will be idle part of time. With the Verlet
+cut-off scheme this load is automatically balanced when the PME load
+is too high (but not when it is too low). This is done by scaling
+the Coulomb cut-off and PME grid spacing by the same amount. In the first
+few hundred steps different settings are tried and the fastest is chosen
+for the rest of the simulation. This does not affect the accuracy of
+the results, but it does affect the decomposition of the Coulomb energy
+into particle and mesh contributions. The auto-tuning can be turned off
+with the option <tt>-notunepme</tt>.
+<p>
+<tt>mdrun</tt> pins (sets affinity of) threads to specific cores,
+when all (logical) cores on a compute node are used by <tt>mdrun</tt>,
+even when no multi-threading is used,
+as this usually results in significantly better performance.
+If the queuing systems or the OpenMP library pinned threads, we honor
+this and don't pin again, even though the layout may be sub-optimal.
+If you want to have <tt>mdrun</tt> override an already set thread affinity
+or pin threads when using less cores, use <tt>-pin on</tt>.
+With SMT (simultaneous multithreading), e.g. Intel Hyper-Threading,
+there are multiple logical cores per physical core.
+The option <tt>-pinstride</tt> sets the stride in logical cores for
+pinning consecutive threads. Without SMT, 1 is usually the best choice.
+With Intel Hyper-Threading 2 is best when using half or less of the
+logical cores, 1 otherwise. The default value of 0 do exactly that:
+it minimizes the threads per logical core, to optimize performance.
+If you want to run multiple mdrun jobs on the same physical node,you should set <tt>-pinstride</tt> to 1 when using all logical cores.
+When running multiple mdrun (or other) simulations on the same physical
+node, some simulations need to start pinning from a non-zero core
+to avoid overloading cores; with <tt>-pinoffset</tt> you can specify
+the offset in logical cores for pinning.
+<p>
+When <tt>mdrun</tt> is started using MPI with more than 1 process
+or with thread-MPI with more than 1 thread, MPI parallelization is used.
+By default domain decomposition is used, unless the <tt>-pd</tt>
+option is set, which selects particle decomposition.
+<p>
With domain decomposition, the spatial decomposition can be set
-with option <tt>-dd</tt>. By default mdrun selects a good decomposition.
+with option <tt>-dd</tt>. By default <tt>mdrun</tt> selects a good decomposition.
The user only needs to change this when the system is very inhomogeneous.
Dynamic load balancing is set with the option <tt>-dlb</tt>,
which can give a significant performance improvement,
this is computationally more efficient starting at about 12 nodes.
The number of PME nodes is set with option <tt>-npme</tt>,
this can not be more than half of the nodes.
-By default mdrun makes a guess for the number of PME
+By default <tt>mdrun</tt> makes a guess for the number of PME
nodes when the number of nodes is larger than 11 or performance wise
not compatible with the PME grid x dimension.
But the user should optimize npme. Performance statistics on this issue
(the simulation will run correctly also when this is not the case).
<p>
This section lists all options that affect the domain decomposition.
-<br>
+<p>
Option <tt>-rdd</tt> can be used to set the required maximum distance
for inter charge-group bonded interactions.
Communication for two-body bonded interactions below the non-bonded
and nearly indepedent of the value of <tt>-rdd</tt>.
With dynamic load balancing option <tt>-rdd</tt> also sets
the lower limit for the domain decomposition cell sizes.
-By default <tt>-rdd</tt> is determined by mdrun based on
+By default <tt>-rdd</tt> is determined by <tt>mdrun</tt> based on
the initial coordinates. The chosen value will be a balance
between interaction range and communication cost.
-<br>
+<p>
When inter charge-group bonded interactions are beyond
-the bonded cut-off distance, mdrun terminates with an error message.
+the bonded cut-off distance, <tt>mdrun</tt> terminates with an error message.
For pair interactions and tabulated bonds
that do not generate exclusions, this check can be turned off
with the option <tt>-noddcheck</tt>.
-<br>
+<p>
When constraints are present, option <tt>-rcon</tt> influences
the cell size limit as well.
Atoms connected by NC constraints, where NC is the LINCS order plus 1,
should not be beyond the smallest cell size. A error message is
generated when this happens and the user should change the decomposition
or decrease the LINCS order and increase the number of LINCS iterations.
-By default mdrun estimates the minimum cell size required for P-LINCS
+By default <tt>mdrun</tt> estimates the minimum cell size required for P-LINCS
in a conservative fashion. For high parallelization it can be useful
to set the distance required for P-LINCS with the option <tt>-rcon</tt>.
-<br>
+<p>
The <tt>-dds</tt> option sets the minimum allowed x, y and/or z scaling
-of the cells with dynamic load balancing. mdrun will ensure that
+of the cells with dynamic load balancing. <tt>mdrun</tt> will ensure that
the cells can scale down by at least this factor. This option is used
for the automated spatial decomposition (when not using <tt>-dd</tt>)
as well as for determining the number of grid pulses, which in turn
This can improve performance for highly parallel simulations
where this global communication step becomes the bottleneck.
For a global thermostat and/or barostat the temperature
-and/or pressure will also only be updated every -gcom steps.
+and/or pressure will also only be updated every <tt>-gcom</tt> steps.
By default it is set to the minimum of nstcalcenergy and nstlist.<p>
With <tt>-rerun</tt> an input trajectory can be given for which
forces and energies will be (re)calculated. Neighbor searching will be
performed for every frame, unless <tt>nstlist</tt> is zero
(see the <tt>.<a href="mdp.html">mdp</a></tt> file).<p>
-ED (essential dynamics) sampling is switched on by using the <tt>-ei</tt>
-flag followed by an <tt>.<a href="edi.html">edi</a></tt> file.
-The <tt>.<a href="edi.html">edi</a></tt> file can be produced using options in the essdyn
-menu of the WHAT IF program. mdrun produces a <tt>.<a href="edo.html">edo</a></tt> file that
+ED (essential dynamics) sampling and/or additional flooding potentials
+are switched on by using the <tt>-ei</tt> flag followed by an <tt>.<a href="edi.html">edi</a></tt>
+file. The <tt>.<a href="edi.html">edi</a></tt> file can be produced with the <tt>make_<a href="edi.html">edi</a></tt> tool
+or by using options in the essdyn menu of the WHAT IF program.
+<tt>mdrun</tt> produces a <tt>.<a href="xvg.html">xvg</a></tt> output file that
contains projections of positions, velocities and forces onto selected
eigenvectors.<p>
When user-defined potential functions have been selected in the
-<tt>.<a href="mdp.html">mdp</a></tt> file the <tt>-table</tt> option is used to pass mdrun
+<tt>.<a href="mdp.html">mdp</a></tt> file the <tt>-table</tt> option is used to pass <tt>mdrun</tt>
a formatted table with potential functions. The file is read from
-either the current directory or from the GMXLIB directory.
-A number of pre-formatted tables are presented in the GMXLIB dir,
-for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard Jones potentials with
+either the current directory or from the <tt>GMXLIB</tt> directory.
+A number of pre-formatted tables are presented in the <tt>GMXLIB</tt> dir,
+for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with
normal Coulomb.
-When pair interactions are present a separate table for pair interaction
+When pair interactions are present, a separate table for pair interaction
functions is read using the <tt>-tablep</tt> option.<p>
When tabulated bonded functions are present in the topology,
interaction functions are read using the <tt>-tableb</tt> option.
For each different tabulated interaction type the table file name is
modified in a different way: before the file extension an underscore is
-appended, then a b for bonds, an a for angles or a d for dihedrals
+appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals
and finally the table number of the interaction type.<p>
The options <tt>-px</tt> and <tt>-pf</tt> are used for writing pull COM
coordinates and forces when pulling is selected
in the <tt>.<a href="mdp.html">mdp</a></tt> file.<p>
-With <tt>-multi</tt> multiple systems are simulated in parallel.
-As many input files are required as the number of systems.
-The system number is appended to the run input and each output filename,
-for instance topol.<a href="tpr.html">tpr</a> becomes topol0.<a href="tpr.html">tpr</a>, topol1.<a href="tpr.html">tpr</a> etc.
+With <tt>-multi</tt> or <tt>-multidir</tt>, multiple systems can be
+simulated in parallel.
+As many input files/directories are required as the number of systems.
+The <tt>-multidir</tt> option takes a list of directories (one for each
+system) and runs in each of them, using the input/output file names,
+such as specified by e.g. the <tt>-s</tt> option, relative to these
+directories.
+With <tt>-multi</tt>, the system number is appended to the run input
+and each output filename, for instance <tt>topol.<a href="tpr.html">tpr</a></tt> becomes
+<tt>topol0.<a href="tpr.html">tpr</a></tt>, <tt>topol1.<a href="tpr.html">tpr</a></tt> etc.
The number of nodes per system is the total number of nodes
divided by the number of systems.
One use of this option is for NMR refinement: when distance
or orientation restraints are present these can be ensemble averaged
over all the systems.<p>
With <tt>-replex</tt> replica exchange is attempted every given number
-of steps. The number of replicas is set with the <tt>-multi</tt> option,
-see above. The <tt>-nex</tt> option turns on Gibbs sampling replica exchange. N^3, where
-N is the number of replicas indicated by <tt>-multi</tt> appears to work relatively well.
-
+of steps. The number of replicas is set with the <tt>-multi</tt> or
+<tt>-multidir</tt> option, described above.
All run input files should use a different coupling temperature,
the order of the files is not important. The random seed is set with
<tt>-reseed</tt>. The velocities are scaled and neighbor searching
is performed after every exchange.<p>
Finally some experimental algorithms can be tested when the
appropriate options have been given. Currently under
-investigation are: polarizability, and X-Ray bombardments.
+investigation are: polarizability and X-ray bombardments.
+<p>
+The option <tt>-membed</tt> does what used to be g_membed, i.e. embed
+a protein into a membrane. The data file should contain the options
+that where passed to g_membed before. The <tt>-mn</tt> and <tt>-mp</tt>
+both apply to this as well.
<p>
The option <tt>-pforce</tt> is useful when you suspect a simulation
crashes due to too large forces. With this option coordinates and
A simulation can be continued by reading the full state from file
with option <tt>-cpi</tt>. This option is intelligent in the way that
if no checkpoint file is found, Gromacs just assumes a normal run and
-starts from the first step of the <a href="tpr.html">tpr</a> file. By default the output
+starts from the first step of the <tt>.<a href="tpr.html">tpr</a></tt> file. By default the output
will be appending to the existing output files. The checkpoint file
contains checksums of all output files, such that you will never
loose data when some output files are modified, corrupt or removed.
-There are three scenarios with <tt>-cpi</tt>:<br>
-* no files with matching names are present: new output files are written<br>
-* all files are present with names and checksums matching those stored
-in the checkpoint file: files are appended<br>
-* otherwise no files are modified and a fatal error is generated<br>
+There are three scenarios with <tt>-cpi</tt>:<p>
+<tt>*</tt> no files with matching names are present: new output files are written<p>
+<tt>*</tt> all files are present with names and checksums matching those stored
+in the checkpoint file: files are appended<p>
+<tt>*</tt> otherwise no files are modified and a fatal error is generated<p>
With <tt>-noappend</tt> new output files are opened and the simulation
part number is added to all output file names.
Note that in all cases the checkpoint file itself is not renamed
file is written at the first neighbor search step where the run time
exceeds <tt>-maxh</tt>*0.99 hours.
<p>
-When mdrun receives a TERM signal, it will set nsteps to the current
-step plus one. When mdrun receives an INT signal (e.g. when ctrl+C is
+When <tt>mdrun</tt> receives a TERM signal, it will set nsteps to the current
+step plus one. When <tt>mdrun</tt> receives an INT signal (e.g. when ctrl+C is
pressed), it will stop after the next neighbor search step
(with nstlist=0 at the next step).
In both cases all the usual output will be written to file.
-When running with MPI, a signal to one of the mdrun processes
+When running with MPI, a signal to one of the <tt>mdrun</tt> processes
is sufficient, this signal should not be sent to mpirun or
-the mdrun process that is the parent of the others.
+the <tt>mdrun</tt> process that is the parent of the others.
<p>
-When mdrun is started with MPI, it does not run niced by default.
+When <tt>mdrun</tt> is started with MPI, it does not run niced by default.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TD ALIGN=RIGHT> <b><tt>-dhdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-field</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> field.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-tabletf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tabletf.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tablep</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tablep.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tableb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpi.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tpid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpidist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html"> sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html"> sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> edsam.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-j</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html"> wham.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-jo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html"> bam.gct</a></tt> </TD><TD> Output, Opt. </TD><TD> General coupling stuff </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> gct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-runav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> runaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-px</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pullx.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-pf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pullf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ro</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rotation.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ra</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">rotangles.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">rotslabs.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">rottorque.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-mtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> nm.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> dipole.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-multidir</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="line_buf.html"> rundir</a></tt> </TD><TD> Input, Opt., Mult. </TD><TD> Run directory </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-membed</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> membed.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> membed.top</a></tt> </TD><TD> Input, Opt. </TD><TD> Topology file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> membed.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-deffnm</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Set the default filename for all file options </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pd</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use particle decompostion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pd</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use particle decompostion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dd</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Domain decomposition grid, 0 is optimize </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nt</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of threads to start (0 is guess) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-npme</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Number of separate nodes to be used for PME, -1 is guess </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ddorder</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>interleave</tt> </TD><TD> DD node order: <tt>interleave</tt>, <tt>pp_pme</tt> or <tt>cartesian</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ddcheck</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Check for all bonded interactions with DD </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-npme</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Number of separate nodes to be used for PME, -1 is guess </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nt</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Total number of threads to start (0 is guess) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ntmpi</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of thread-MPI threads to start (0 is guess) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ntomp</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of OpenMP threads per MPI process/thread to start (0 is guess) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ntomp_pme</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of OpenMP threads per MPI process/thread to start (0 is -ntomp) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pin</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Fix threads (or processes) to specific cores: <tt>auto</tt>, <tt>on</tt> or <tt>off</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pinoffset</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pinstride</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-gpu_id</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> List of GPU id's to use </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ddcheck</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Check for all bonded interactions with DD </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rdd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rcon</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance for P-LINCS (nm), 0 is estimate </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dlb</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Dynamic load balancing (with DD): <tt>auto</tt>, <tt>no</tt> or <tt>yes</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dds</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.8 </tt> </TD><TD> Minimum allowed dlb scaling of the DD cell size </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-gcom</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Global communication frequency </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Write a compact <a href="log.html">log</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]seppot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write separate V and dVdl terms for each interaction type and node to the <a href="log.html">log</a> file(s) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nb</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Calculate non-bonded interactions on: <tt>auto</tt>, <tt>cpu</tt>, <tt>gpu</tt> or <tt>gpu_cpu</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]tunepme</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Optimize PME load between PP/PME nodes or GPU/CPU </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]testverlet</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Test the Verlet non-bonded scheme </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Write a compact <a href="log.html">log</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]seppot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write separate V and dVdl terms for each interaction type and node to the <a href="log.html">log</a> file(s) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-pforce</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Print all forces larger than this (kJ/mol nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]reprod</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Try to avoid optimizations that affect binary reproducibility </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]reprod</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Try to avoid optimizations that affect binary reproducibility </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cpt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>15 </tt> </TD><TD> Checkpoint interval (minutes) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]cpnum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Keep and number checkpoint files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]append</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cpnum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Keep and number checkpoint files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]append</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-2</tt> </TD><TD> Run this number of steps, overrides .<a href="mdp.html">mdp</a> file option </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-maxh</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Terminate after 0.99 times this time (hours) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-multi</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Do multiple simulations in parallel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-replex</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Attempt replica exchange every # steps </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nex</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Attempt $N$ Gibbs sampling replica exchanges at every exchange interval. $N^3$ is a suggested frequency. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-replex</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Attempt replica exchange periodically with this period (steps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nex</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-reseed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Seed for replica exchange, -1 is generate a seed </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ionize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a simulation including the effect of an X-Ray bombardment on your system </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ionize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a simulation including the effect of an X-Ray bombardment on your system </TD></TD>
</TABLE>
<P>
<hr>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Methanol</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<P><H2>Methanol</A></H2>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Methanol+Water</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<P><H2>Methanol+Water</A></H2>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mk_angndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-mk_angndx makes an index file for calculation of
+<tt>mk_angndx</tt> makes an index file for calculation of
angle distributions etc. It uses a run input file (<tt>.tpx</tt>) for the
definitions of the angles, dihedrals etc.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle: <tt>angle</tt>, <tt>dihedral</tt>, <tt>improper</tt> or <tt>ryckaert-bellemans</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]hyd</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Include angles with atoms with mass < 1.5 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-hq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Ignore angles with atoms with mass < 1.5 and |q| < hq </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]hyd</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Include angles with atoms with mass < 1.5 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-hq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Files with the mtx file extension contain a matrix.
The file format is identical to the <a href="trj.html">trj</a> format.
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The GROMACS index file (usually called index.ndx) contains some
user definable sets of atoms. The file can be read by
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Files with the out file extension contain generic output. As it is not possible
to categorise all data file formats, GROMACS has a generic file format called
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Files with the <a href="pdb.html">.pdb</a> extension are molecular
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>pdb2gmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-This program reads a <a href="pdb.html">pdb</a> (or <a href="gro.html">gro</a>) file, reads
+This program reads a <tt>.<a href="pdb.html">pdb</a></tt> (or <tt>.<a href="gro.html">gro</a></tt>) file, reads
some database files, adds hydrogens to the molecules and generates
-coordinates in Gromacs (Gromos), or optionally <a href="pdb.html">pdb</a>, format
-and a topology in Gromacs format.
+coordinates in GROMACS (GROMOS), or optionally <tt>.<a href="pdb.html">pdb</a></tt>, format
+and a topology in GROMACS format.
These files can subsequently be processed to generate a run input file.
<p>
-pdb2gmx will search for force fields by looking for
+<tt>pdb2gmx</tt> will search for force fields by looking for
a <tt>forcefield.<a href="itp.html">itp</a></tt> file in subdirectories <tt><forcefield>.ff</tt>
-of the current working directory and of the Gomracs library directory
+of the current working directory and of the GROMACS library directory
as inferred from the path of the binary or the <tt>GMXLIB</tt> environment
variable.
By default the forcefield selection is interactive,
but you can use the <tt>-ff</tt> option to specify one of the short names
-in the list on the command line instead. In that case pdb2gmx just looks
+in the list on the command line instead. In that case <tt>pdb2gmx</tt> just looks
for the corresponding <tt><forcefield>.ff</tt> directory.
<p>
After choosing a force field, all files will be read only from
the corresponding force field directory.
If you want to modify or add a residue types, you can copy the force
-field directory from the Gromacs library directory to your current
+field directory from the GROMACS library directory to your current
working directory. If you want to add new protein residue types,
-you will need to modify residuetypes.<a href="dat.html">dat</a> in the libary directory
+you will need to modify <tt>residuetypes.<a href="dat.html">dat</a></tt> in the library directory
or copy the whole library directory to a local directory and set
the environment variable <tt>GMXLIB</tt> to the name of that directory.
-Check chapter 5 of the manual for more information about file formats.
+Check Chapter 5 of the manual for more information about file formats.
<p>
-Note that a <a href="pdb.html">pdb</a> file is nothing more than a file format, and it
+Note that a <tt>.<a href="pdb.html">pdb</a></tt> file is nothing more than a file format, and it
need not necessarily contain a protein structure. Every kind of
molecule for which there is support in the database can be converted.
If there is no support in the database, you can add it yourself.<p>
The program has limited intelligence, it reads a number of database
files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.),
if necessary this can be done manually. The program can prompt the
-user to select which kind of LYS, ASP, GLU, CYS or HIS residue she
-wants. For LYS the choice is between neutral (two protons on NZ) or
-protonated (three protons, default), for ASP and GLU unprotonated
-(default) or protonated, for HIS the proton can be either on ND1,
+user to select which kind of LYS, ASP, GLU, CYS or HIS residue is
+desired. For Lys the choice is between neutral (two protons on NZ) or
+protonated (three protons, default), for Asp and Glu unprotonated
+(default) or protonated, for His the proton can be either on ND1,
on NE2 or on both. By default these selections are done automatically.
For His, this is based on an optimal hydrogen bonding
conformation. Hydrogen bonds are defined based on a simple geometric
-criterium, specified by the maximum hydrogen-donor-acceptor angle
+criterion, specified by the maximum hydrogen-donor-acceptor angle
and donor-acceptor distance, which are set by <tt>-angle</tt> and
<tt>-dist</tt> respectively.<p>
+The protonation state of N- and C-termini can be chosen interactively
+with the <tt>-ter</tt> flag. Default termini are ionized (NH3+ and COO-),
+respectively. Some force fields support zwitterionic forms for chains of
+one residue, but for polypeptides these options should NOT be selected.
+The AMBER force fields have unique forms for the terminal residues,
+and these are incompatible with the <tt>-ter</tt> mechanism. You need
+to prefix your N- or C-terminal residue names with "N" or "C"
+respectively to use these forms, making sure you preserve the format
+of the coordinate file. Alternatively, use named terminating residues
+(e.g. ACE, NME).<p>
The separation of chains is not entirely trivial since the markup
in user-generated PDB files frequently varies and sometimes it
is desirable to merge entries across a TER record, for instance
if you want a disulfide bridge or distance restraints between
two protein chains or if you have a HEME group bound to a protein.
In such cases multiple chains should be contained in a single
-<tt>molecule_type</tt> definition.
-To handle this, pdb2gmx has an option <tt>-chainsep</tt> so you can
-choose whether a new chain should start when we find a TER record,
-when the chain id changes, combinations of either or both of these
-or fully interactively.<p>
-pdb2gmx will also check the occupancy field of the <a href="pdb.html">pdb</a> file.
+<tt>moleculetype</tt> definition.
+To handle this, <tt>pdb2gmx</tt> uses two separate options.
+First, <tt>-chainsep</tt> allows you to choose when a new chemical chain should
+start, and termini added when applicable. This can be done based on the
+existence of TER records, when the chain id changes, or combinations of either
+or both of these. You can also do the selection fully interactively.
+In addition, there is a <tt>-merge</tt> option that controls how multiple chains
+are merged into one moleculetype, after adding all the chemical termini (or not).
+This can be turned off (no merging), all non-water chains can be merged into a
+single molecule, or the selection can be done interactively.<p>
+<tt>pdb2gmx</tt> will also check the occupancy field of the <tt>.<a href="pdb.html">pdb</a></tt> file.
If any of the occupancies are not one, indicating that the atom is
not resolved well in the structure, a warning message is issued.
-When a <a href="pdb.html">pdb</a> file does not originate from an X-Ray structure determination
+When a <tt>.<a href="pdb.html">pdb</a></tt> file does not originate from an X-ray structure determination
all occupancy fields may be zero. Either way, it is up to the user
to verify the correctness of the input data (read the article!).<p>
-During processing the atoms will be reordered according to Gromacs
+During processing the atoms will be reordered according to GROMACS
conventions. With <tt>-n</tt> an index file can be generated that
contains one group reordered in the same way. This allows you to
-convert a Gromos trajectory and coordinate file to Gromos. There is
+convert a GROMOS trajectory and coordinate file to GROMOS. There is
one limitation: reordering is done after the hydrogens are stripped
from the input and before new hydrogens are added. This means that
you should not use <tt>-ignh</tt>.<p>
The <tt>.<a href="gro.html">gro</a></tt> and <tt>.<a href="g96.html">g96</a></tt> file formats do not support chain
-identifiers. Therefore it is useful to enter a <a href="pdb.html">pdb</a> file name at
-the <tt>-o</tt> option when you want to convert a multichain <a href="pdb.html">pdb</a> file.
+identifiers. Therefore it is useful to enter a <tt>.<a href="pdb.html">pdb</a></tt> file name at
+the <tt>-o</tt> option when you want to convert a multi-chain <tt>.<a href="pdb.html">pdb</a></tt> file.
<p>
The option <tt>-vsite</tt> removes hydrogen and fast improper dihedral
motions. Angular and out-of-plane motions can be removed by changing
hydrogens into virtual sites and fixing angles, which fixes their
position relative to neighboring atoms. Additionally, all atoms in the
aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)
-can be converted into virtual sites, elminating the fast improper dihedral
-fluctuations in these rings. Note that in this case all other hydrogen
+can be converted into virtual sites, eliminating the fast improper dihedral
+fluctuations in these rings. <b>Note</b> that in this case all other hydrogen
atoms are also converted to virtual sites. The mass of all atoms that are
converted into virtual sites, is added to the heavy atoms.<p>
Also slowing down of dihedral motion can be done with <tt>-heavyh</tt>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-chainsep</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>id_or_ter</tt> </TD><TD> Condition in PDB files when a new chain and molecule_type should be started: <tt>id_or_ter</tt>, <tt>id_and_ter</tt>, <tt>ter</tt>, <tt>id</tt> or <tt>interactive</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ff</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>select</tt> </TD><TD> Force field, interactive by default. Use -h for information. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-chainsep</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>id_or_ter</tt> </TD><TD> Condition in PDB files when a new chain should be started (adding termini): <tt>id_or_ter</tt>, <tt>id_and_ter</tt>, <tt>ter</tt>, <tt>id</tt> or <tt>interactive</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-merge</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Merge multiple chains into a single [moleculetype]: <tt>no</tt>, <tt>all</tt> or <tt>interactive</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ff</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>select</tt> </TD><TD> Force field, interactive by default. Use <tt>-h</tt> for information. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-water</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>select</tt> </TD><TD> Water model to use: <tt>select</tt>, <tt>none</tt>, <tt>spc</tt>, <tt>spce</tt>, <tt>tip3p</tt>, <tt>tip4p</tt> or <tt>tip5p</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]inter</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set the next 8 options to interactive </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ss</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive SS bridge selection </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ter</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive termini selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]lys</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Lysine selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]arg</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Arganine selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]asp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Aspartic Acid selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]glu</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Glutamic Acid selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]gln</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Glutamine selection, iso neutral </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]his</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Histidine selection, iso checking H-bonds </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]inter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set the next 8 options to interactive </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ss</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive SS bridge selection </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive termini selection, instead of charged (default) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lys</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive lysine selection, instead of charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]arg</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive arginine selection, instead of charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]asp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive aspartic acid selection, instead of charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]glu</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive glutamic acid selection, instead of charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]gln</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive glutamine selection, instead of neutral </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]his</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive histidine selection, instead of checking H-bonds </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-angle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>135 </tt> </TD><TD> Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.3 </tt> </TD><TD> Maximum donor-acceptor distance for a H-bond (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]una</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ignh</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Ignore hydrogen atoms that are in the <a href="pdb.html">pdb</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]missing</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Continue when atoms are missing, dangerous </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be slightly more verbose in messages </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]una</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ignh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Ignore hydrogen atoms that are in the coordinate file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]missing</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Continue when atoms are missing, dangerous </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be slightly more verbose in messages </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-posrefc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000 </tt> </TD><TD> Force constant for position restraints </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-vsite</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Convert atoms to virtual sites: <tt>none</tt>, <tt>hydrogens</tt> or <tt>aromatics</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]heavyh</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Make hydrogen atoms heavy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]deuterate</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change the mass of hydrogens to 2 amu </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]chargegrp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use charge groups in the <a href="rtp.html">rtp</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]cmap</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use cmap torsions (if enabled in the <a href="rtp.html">rtp</a> file) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]renum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Renumber the residues consecutively in the output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rtpres</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use <a href="rtp.html">rtp</a> entry names as residue names </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]heavyh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Make hydrogen atoms heavy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]deuterate</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change the mass of hydrogens to 2 amu </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]chargegrp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use charge groups in the <tt>.<a href="rtp.html">rtp</a></tt> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cmap</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use cmap torsions (if enabled in the <tt>.<a href="rtp.html">rtp</a></tt> file) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]renum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Renumber the residues consecutively in the output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rtpres</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use <tt>.<a href="rtp.html">rtp</a></tt> entry names as residue names </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>protonate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Protein unfolding</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<h3>Protein unfolding</h3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The rtp file extension stands for residue toplogy.
Such a file is needed by <a href="pdb2gmx.html">pdb2gmx</a>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Peptide</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<h2>Contents</h2>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
We use <b>LaTeX</b> for <i>document</i> processing.
Although the input is not so
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The top file extension stands for topology. It is an ascii file which is
read by <a href="grompp.html">grompp</a> which processes it
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The tpa file extension stands for binary run input file. This file contains
the starting structure of your simulation, The molecular topology and
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
</body>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The tpb file extension stands for binary run input file. This file contains
the starting structure of your simulation, The molecular topology and
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
</body>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>tpbconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
tpbconv can edit run input files in four ways.<p>
-<b>1st.</b> by modifying the number of steps in a run input file
+<b>1.</b> by modifying the number of steps in a run input file
with options <tt>-extend</tt>, <tt>-until</tt> or <tt>-nsteps</tt>
(nsteps=-1 means unlimited number of steps)<p>
-<b>2nd.</b> (OBSOLETE) by creating a run input file
+<b>2.</b> (OBSOLETE) by creating a run input file
for a continuation run when your simulation has crashed due to e.g.
a full disk, or by making a continuation run input file.
This option is obsolete, since <a href="mdrun.html">mdrun</a> now writes and reads
checkpoint files.
-Note that a frame with coordinates and velocities is needed.
+<b>Note</b> that a frame with coordinates and velocities is needed.
When pressure and/or Nose-Hoover temperature coupling is used
an energy file can be supplied to get an exact continuation
of the original run.<p>
-<b>3rd.</b> by creating a tpx file for a subset of your original
+<b>3.</b> by creating a <tt>.tpx</tt> file for a subset of your original
tpx file, which is useful when you want to remove the solvent from
-your tpx file, or when you want to make e.g. a pure Ca tpx file.
-<b>WARNING: this tpx file is not fully functional</b>.
-<b>4th.</b> by setting the charges of a specified group
+your <tt>.tpx</tt> file, or when you want to make e.g. a pure Cα <tt>.tpx</tt> file.
+Note that you may need to use <tt>-nsteps -1</tt> (or similar) to get
+this to work.
+<b>WARNING: this <tt>.tpx</tt> file is not fully functional</b>.<p>
+<b>4.</b> by setting the charges of a specified group
to zero. This is useful when doing free energy estimates
using the LIE (Linear Interaction Energy) method.
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-extend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Extend runtime by this amount (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-until</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Extend runtime until this ending time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Change the number of steps </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Continue from frame at this time (ps) instead of the last frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroq</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set the charges of a group (from the index) to zero </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Require velocities from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]cont</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> For exact continuation, the constraints should not be applied before the first step </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroq</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set the charges of a group (from the index) to zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Require velocities from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cont</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> For exact continuation, the constraints should not be applied before the first step </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-init_fep_state</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> fep state to initialize from </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The tpr file extension stands for portable binary run input file. This file
contains the starting structure of your simulation, the molecular topology
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Files with the trj file extension contain the trajectory of a simulation.
In this file all the coordinates, velocities, forces and energies are
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjcat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-trjcat concatenates several input trajectory files in sorted order.
+<tt>trjcat</tt> concatenates several input trajectory files in sorted order.
In case of double time frames the one in the later file is used.
By specifying <tt>-settime</tt> you will be asked for the start time
of each file. The input files are taken from the command line,
-such that a command like <tt>trjcat -
o fixed.<a href="trr.html">trr</a> *.<a href="trr.html">trr</a></tt> should do
-the trick. Using <tt>-cat</tt> you can simply paste several files
+such that a command like <tt>trjcat -
f *.<a href="trr.html">trr</a> -o fixed.<a href="trr.html">trr</a></tt> should do
+the trick. Using <tt>-cat</tt>, you can simply paste several files
together without removal of frames with identical time stamps.<p>
One important option is inferred when the output file is amongst the
input files. In that case that particular file will be appended to
Obviously the file to append to has to be the one with lowest starting
time since one can only append at the end of a file.<p>
If the <tt>-demux</tt> option is given, the N trajectories that are
-read, are written in another order as specified in the <a href="xvg.html">xvg</a> file.
-The <
a href="xvg.html">xvg</a> file should contain something like:<p>
-0 0 1 2 3 4 5<br>
-2 1 0 2 3 5 4<br>
+read, are written in another order as specified in the <tt>.<a href="xvg.html">xvg</a></tt> file.
+The <
tt>.<a href="xvg.html">xvg</a></tt> file should contain something like:<p>
+<tt>0 0 1 2 3 4 5<br>
+2 1 0 2 3 5 4</tt><br>
Where the first number is the time, and subsequent numbers point to
trajectory indices.
The frames corresponding to the numbers present at the first line
are collected into the output trajectory. If the number of frames in
-the trajectory does not match that in the <a href="xvg.html">xvg</a> file then the program
+the trajectory does not match that in the <tt>.<a href="xvg.html">xvg</a></tt> file then the program
tries to be smart. Beware.
<P>
<H3>Files</H3>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> First time to use (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Last time to use (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only write frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-prec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Precision for .<a href="xtc.html">xtc</a> and .<a href="gro.html">gro</a> writing in number of decimal places </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Read and write velocities if possible </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change starting time interactively </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Sort trajectory files (not frames) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]keeplast</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> keep overlapping frames at end of trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]overwrite</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> overwrite overlapping frames during appending </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]cat</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> do not discard double time frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-prec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Precision for <tt>.<a href="xtc.html">xtc</a></tt> and <tt>.<a href="gro.html">gro</a></tt> writing in number of decimal places </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Read and write velocities if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change starting time interactively </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Sort trajectory files (not frames) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]keeplast</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Keep overlapping frames at end of trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]overwrite</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Overwrite overlapping frames during appending </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cat</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do not discard double time frames </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-trjconv can convert trajectory files in many ways:<br>
+<tt>trjconv</tt> can convert trajectory files in many ways:<br>
<b>1.</b> from one format to another<br>
<b>2.</b> select a subset of atoms<br>
<b>3.</b> change the periodicity representation<br>
(<tt>-t0</tt> and <tt>-timestep</tt>)<br>
<b>9.</b> cut the trajectory in small subtrajectories according
to information in an index file. This allows subsequent analysis of
-the subtrajectories that could, for example be the result of a
+the subtrajectories that could, for example, be the result of a
cluster analysis. Use option <tt>-sub</tt>.
This assumes that the entries in the index file are frame numbers and
dumps each group in the index file to a separate trajectory file.<br>
<b>10.</b> select frames within a certain range of a quantity given
in an <tt>.<a href="xvg.html">xvg</a></tt> file.<p>
-The program <tt><a href="trjcat.html">trjcat</a></tt> can concatenate multiple trajectory files.
+The program <tt><a href="trjcat.html">trjcat</a></tt> is better suited for concatenating multiple trajectory files.
<p>
Currently seven formats are supported for input and output:
<tt>.<a href="xtc.html">xtc</a></tt>, <tt>.<a href="trr.html">trr</a></tt>, <tt>.<a href="trj.html">trj</a></tt>, <tt>.<a href="gro.html">gro</a></tt>, <tt>.<a href="g96.html">g96</a></tt>,
is always taken from <tt>-ndec</tt>, when this option is set.
All other formats have fixed precision. <tt>.<a href="trr.html">trr</a></tt> and <tt>.<a href="trj.html">trj</a></tt>
output can be single or double precision, depending on the precision
-of the trjconv binary.
+of the <tt>trjconv</tt> binary.
Note that velocities are only supported in
<tt>.<a href="trr.html">trr</a></tt>, <tt>.<a href="trj.html">trj</a></tt>, <tt>.<a href="gro.html">gro</a></tt> and <tt>.<a href="g96.html">g96</a></tt> files.<p>
Option <tt>-app</tt> can be used to
No checks are performed to ensure integrity
of the resulting combined trajectory file.<p>
Option <tt>-sep</tt> can be used to write every frame to a separate
-.<a href="gro.html">gro</a>, .<a href="g96.html">g96</a> or .<a href="pdb.html">pdb</a> file, default all frames all written to one file.
+<tt>.<a href="gro.html">gro</a>, .<a href="g96.html">g96</a></tt> or <tt>.<a href="pdb.html">pdb</a></tt> file. By default, all frames all written to one file.
<tt>.<a href="pdb.html">pdb</a></tt> files with all frames concatenated can be viewed with
<tt>rasmol -nmrpdb</tt>.<p>
It is possible to select part of your trajectory and write it out
We recommend to use the portable <tt>.<a href="xtc.html">xtc</a></tt> format for your analysis
to save disk space and to have portable files.<p>
There are two options for fitting the trajectory to a reference
-either for essential dynamics analysis or for whatever.
+either for essential dynamics analysis, etc.
The first option is just plain fitting to a reference structure
-in the structure file, the second option is a progressive fit
+in the structure file. The second option is a progressive fit
in which the first timeframe is fitted to the reference structure
in the structure file to obtain and each subsequent timeframe is
fitted to the previously fitted structure. This way a continuous
conformational transitions.<p>
Option <tt>-pbc</tt> sets the type of periodic boundary condition
treatment:<br>
-* <tt>mol</tt> puts the center of mass of molecules in the box.<br>
-* <tt>res</tt> puts the center of mass of residues in the box.<br>
-* <tt>atom</tt> puts all the atoms in the box.<br>
-* <tt>nojump</tt> checks if atoms jump across the box and then puts
+<tt>* mol</tt> puts the center of mass of molecules in the box,
+and requires a run input file to be supplied with <tt>-s</tt>.<br>
+<tt>* res</tt> puts the center of mass of residues in the box.<br>
+<tt>* atom</tt> puts all the atoms in the box.<br>
+<tt>* nojump</tt> checks if atoms jump across the box and then puts
them back. This has the effect that all molecules
will remain whole (provided they were whole in the initial
-conformation), note that this ensures a continuous trajectory but
+conformation). <b>Note</b> that this ensures a continuous trajectory but
molecules may diffuse out of the box. The starting configuration
for this procedure is taken from the structure file, if one is
supplied, otherwise it is the first frame.<br>
-* <tt>cluster</tt> clusters all the atoms in the selected index
-such that they are all closest to the center of mass of the cluster
-which is iteratively updated. Note that this will only give meaningful
+<tt>* cluster</tt> clusters all the atoms in the selected index
+such that they are all closest to the center of mass of the cluster,
+which is iteratively updated. <b>Note</b> that this will only give meaningful
results if you in fact have a cluster. Luckily that can be checked
afterwards using a trajectory viewer. Note also that if your molecules
are broken this will not work either.<br>
-* <tt>whole</tt> only makes broken molecules whole.<p>
+The separate option <tt>-clustercenter</tt> can be used to specify an
+approximate center for the cluster. This is useful e.g. if you have
+two big vesicles, and you want to maintain their relative positions.<br>
+<tt>* whole</tt> only makes broken molecules whole.<p>
Option <tt>-ur</tt> sets the unit cell representation for options
<tt>mol</tt>, <tt>res</tt> and <tt>atom</tt> of <tt>-pbc</tt>.
All three options give different results for triclinic boxes and
<tt>rect</tt> is the ordinary brick shape.
<tt>tric</tt> is the triclinic unit cell.
<tt>compact</tt> puts all atoms at the closest distance from the center
-of the box. This can be useful for visualizing e.g. truncated
-octahedrons. The center for options <tt>tric</tt> and <tt>compact</tt>
+of the box. This can be useful for visualizing e.g. truncated octahedra
+or rhombic dodecahedra. The center for options <tt>tric</tt> and <tt>compact</tt>
is <tt>tric</tt> (see below), unless the option <tt>-boxcenter</tt>
is set differently.<p>
Option <tt>-center</tt> centers the system in the box. The user can
<tt>zero</tt>: zero.
Use option <tt>-pbc mol</tt> in addition to <tt>-center</tt> when you
want all molecules in the box after the centering.<p>
-With <tt>-dt</tt> it is possible to reduce the number of
+It is not always possible to use combinations of <tt>-pbc</tt>,
+<tt>-fit</tt>, <tt>-ur</tt> and <tt>-center</tt> to do exactly what
+you want in one call to <tt>trjconv</tt>. Consider using multiple
+calls, and check out the GROMACS website for suggestions.<p>
+With <tt>-dt</tt>, it is possible to reduce the number of
frames in the output. This option relies on the accuracy of the times
in your input trajectory, so if these are inaccurate use the
<tt>-timestep</tt> option to modify the time (this can be done
-simultaneously). For making smooth movies the program <tt><a href="g_filter.html">g_filter</a></tt>
+simultaneously). For making smooth movies
, the program <tt><a href="g_filter.html">g_filter</a></tt>
can reduce the number of frames while using low-pass frequency
filtering, this reduces aliasing of high frequency motions.<p>
-Using <tt>-trunc</tt>
trjconv can truncate <tt>.<a href="trj.html">trj</a></tt> in place, i.e.
+Using <tt>-trunc</tt>
<tt>trjconv</tt> can truncate <tt>.<a href="trj.html">trj</a></tt> in place, i.e.
without copying the file. This is useful when a run has crashed
-during disk I/O (one more disk full), or when two contiguous
-trajectories must be concatenated without have double frames.<p>
-<tt><a href="trjcat.html">trjcat</a></tt> is more suitable for concatenating trajectory files.<p>
+during disk I/O (i.e. full disk), or when two contiguous
+trajectories must be concatenated without having double frames.<p>
Option <tt>-dump</tt> can be used to extract a frame at or near
one specific time from your trajectory.<p>
Option <tt>-drop</tt> reads an <tt>.<a href="xvg.html">xvg</a></tt> file with times and values.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only write frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Round measurements to nearest picosecond </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Round measurements to nearest picosecond </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dump</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Dump frame nearest specified time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-t0</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Starting time (ps) (default: don't change) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-timestep</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Change time step between input frames (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-pbc</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> PBC treatment (see help text for full description): <tt>none</tt>, <tt>mol</tt>, <tt>res</tt>, <tt>atom</tt>, <tt>nojump</tt>, <tt>cluster</tt> or <tt>whole</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ur</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rect</tt> </TD><TD> Unit-cell representation: <tt>rect</tt>, <tt>tric</tt> or <tt>compact</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]center</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Center atoms in box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]center</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Center atoms in box </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-boxcenter</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>tric</tt> </TD><TD> Center for -pbc and -center: <tt>tric</tt>, <tt>rect</tt> or <tt>zero</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Size for new cubic box (default: read from input) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-clustercenter</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Optional starting point for pbc cluster option </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-trans</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> All coordinates will be translated by trans. This can advantageously be combined with -pbc mol -ur compact. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-shift</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> All coordinates will be shifted by framenr*shift </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit molecule to ref structure in the structure file: <tt>none</tt>, <tt>rot+trans</tt>, <tt>rotxy+transxy</tt>, <tt>translation</tt>, <tt>transxy</tt> or <tt>progressive</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ndec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Precision for .<a href="xtc.html">xtc</a> and .<a href="gro.html">gro</a> writing in number of decimal places </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Read and write velocities if possible </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]force</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Read and write forces if possible </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-trunc</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Truncate input <a href="trj.html">trj</a> file after this time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Read and write velocities if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]force</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Read and write forces if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trunc</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Truncate input trajectory file after this time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-exec</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Execute command for every output frame with the frame number as argument </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]app</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Append output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]app</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Append output </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-split</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Start writing new file when t MOD split = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT>
gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write each frame to a separate .<a href="gro.html">gro</a>, .<a href="g96.html">g96</a> or .<a href="pdb.html">pdb</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nzero</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Prepend file number in case you use the -sep flag with this number of zeroes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write each frame to a separate .<a href="gro.html">gro</a>, .<a href="g96.html">g96</a> or .<a href="pdb.html">pdb</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nzero</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> If the -sep flag is set, use these many digits for the file numbers and prepend zeros as needed </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dropunder</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Drop all frames below this value </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dropover</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Drop all frames above this value </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]conect</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Add conect records when writing <a href="pdb.html">pdb</a> files. Useful for visualization of non-standard molecules, e.g. coarse grained ones </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]conect</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Add conect records when writing <tt>.<a href="pdb.html">pdb</a></tt> files. Useful for visualization of non-standard molecules, e.g. coarse grained ones </TD></TD>
</TABLE>
<P>
<hr>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjorder</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-trjorder orders molecules according to the smallest distance
+<tt>trjorder</tt> orders molecules according to the smallest distance
to atoms in a reference group
or on z-coordinate (with option <tt>-z</tt>).
With distance ordering, it will ask for a group of reference
be used instead of a reference atom by setting <tt>-da</tt> to 0.
All atoms in the trajectory are written
to the output trajectory.<p>
-trjorder can be useful for e.g. analyzing the n waters closest to a
+<tt>trjorder</tt> can be useful for e.g. analyzing the n waters closest to a
protein.
In that case the reference group would be the protein and the group
of molecules would consist of all the water atoms. When an index group
of the first n waters is made, the ordered trajectory can be used
with any Gromacs program to analyze the n closest waters.
<p>
-If the output file is a <a href="pdb.html">pdb</a> file, the distance to the reference target
-will be stored in the B-factor field in order to color with e.g. rasmol.
+If the output file is a <tt>.<a href="pdb.html">pdb</a></tt> file, the distance to the reference target
+will be stored in the B-factor field in order to color with e.g. Rasmol.
<p>
With option <tt>-nshell</tt> the number of molecules within a shell
of radius <tt>-r</tt> around the reference group are printed.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-na</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of atoms in a molecule </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-da</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Atom used for the distance calculation, 0 is COM </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the distance to the center of mass of the reference group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the distance to the center of mass of the reference group </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Order molecules on z-coordinate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Order molecules on z-coordinate </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Files with the trr file extension contain the trajectory of a simulation.
In this file all the coordinates, velocities, forces and energies are
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Water</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<P><H2><A NAME="water">Water</A></H2>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>wheel</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>x2top</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The GROMACS xpm file format is compatible with the XPixMap format
and is used for storing matrix data.
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xpm2ps</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-xpm2ps makes a beautiful color plot of an XPixelMap file.
+<tt>xpm2ps</tt> makes a beautiful color plot of an XPixelMap file.
Labels and axis can be displayed, when they are supplied
in the correct matrix format.
-Matrix data may be generated by programs such as <a href="do_dssp.html">do_dssp</a>, <a href="g_rms.html">g_rms</a> or
-<
a href="g_mdmat.html">g_mdmat</a>.<p>
-Parameters are set in the <tt><a href="m2p.html">m2p</a></tt> file optionally supplied with
-<tt>-di</tt>. Reasonable defaults are provided. Settings for the y-axis
-default to those for the x-axis. Font names have a defaulting hierarchy:
+Matrix data may be generated by programs such as <tt><a href="do_dssp.html">do_dssp</a></tt>, <tt><a href="g_rms.html">g_rms</a></tt> or
+<
tt><a href="g_mdmat.html">g_mdmat</a></tt>.<p>
+Parameters are set in the <tt>
.<a href="m2p.html">m2p</a></tt> file optionally supplied with
+<tt>-di</tt>. Reasonable defaults are provided. Settings for the <it>y</it>-axis
+default to those for the <it>x</it>-axis. Font names have a defaulting hierarchy:
titlefont -> legendfont; titlefont -> (xfont -> yfont -> ytickfont)
-> xtickfont, e.g. setting titlefont sets all fonts, setting xfont
sets yfont, ytickfont and xtickfont.<p>
-When no <tt><a href="m2p.html">m2p</a></tt> file is supplied, many setting are set by
-command line options. The most important option is <tt>-size</tt>
+When no <tt>.<a href="m2p.html">m2p</a></tt> file is supplied, many settings are taken from
+command line options. The most important option is <tt>-size</tt>,
which sets the size of the whole matrix in postscript units.
This option can be overridden with the <tt>-bx</tt> and <tt>-by</tt>
-options (and the corresponding parameters in the <tt><a href="m2p.html">m2p</a></tt> file),
+options (and the corresponding parameters in the <tt>
.<a href="m2p.html">m2p</a></tt> file),
which set the size of a single matrix element.<p>
-With <tt>-f2</tt> a 2nd matrix file can be supplied, both matrix
+With <tt>-f2</tt> a second matrix file can be supplied. Both matrix
files will be read simultaneously and the upper left half of the
first one (<tt>-f</tt>) is plotted together with the lower right
half of the second one (<tt>-f2</tt>). The diagonal will contain
If the color coding and legend labels of both matrices are identical,
only one legend will be displayed, else two separate legends are
displayed.
-With <tt>-combine</tt> an alternative operation can be selected
+With <tt>-combine</tt>, an alternative operation can be selected
to combine the matrices. The output range is automatically set
to the actual range of the combined matrix. This can be overridden
with <tt>-cmin</tt> and <tt>-cmax</tt>.<p>
<tt>-title</tt> can be set to <tt>none</tt> to suppress the title, or to
<tt>ylabel</tt> to show the title in the Y-label position (alongside
-With the <tt>-rainbow</tt> option dull grey-scale matrices can be turned
+the
<it>y</it>-axis).<p>
+With the <tt>-rainbow</tt> option, dull grayscale matrices can be turned
into attractive color pictures.<p>
Merged or rainbowed matrices can be written to an XPixelMap file with
the <tt>-<a href="xpm.html">xpm</a></tt> option.
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]frame</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Display frame, ticks, labels, title and legend </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]frame</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Display frame, ticks, labels, title and legend </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-title</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>top</tt> </TD><TD> Show title at: <tt><a href="top.html">top</a></tt>, <tt>once</tt>, <tt>ylabel</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]yonce</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Show y-label only once </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]yonce</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Show y-label only once </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-legend</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>both</tt> </TD><TD> Show legend: <tt>both</tt>, <tt>first</tt>, <tt>second</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-diag</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>first</tt> </TD><TD> Diagonal: <tt>first</tt>, <tt>second</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-size</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400 </tt> </TD><TD> Horizontal size of the matrix in ps units </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bx</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Element x-size, overrides -size (also y-size when -by is not set) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bx</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Element x-size, overrides <tt>-size</tt> (also y-size when <tt>-by</tt> is not set) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-by</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Element y-size </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rainbow</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Rainbow colors, convert white to: <tt>no</tt>, <tt>blue</tt> or <tt>red</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-gradient</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Re-scale colormap to a smooth gradient from white {1,1,1} to {r,g,b} </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> only write out every nr-th row and column </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroline</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> insert line in <a href="xpm.html">xpm</a> matrix where axis label is zero </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-legoffset</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip first N colors from <a href="xpm.html">xpm</a> file for the legend </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroline</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> insert line in <tt>.<a href="xpm.html">xpm</a></tt> matrix where axis label is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-legoffset</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip first N colors from <tt>.<a href="xpm.html">xpm</a></tt> file for the legend </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-combine</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>halves</tt> </TD><TD> Combine two matrices: <tt>halves</tt>, <tt>add</tt>, <tt>sub</tt>, <tt>mult</tt> or <tt>div</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum for combination output </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum for combination output </TD></TD>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xrama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The xtc format is a <b>portable</b> format for trajectories.
It uses the <i>xdr</i> routines for writing and reading
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
+<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Almost all output from GROMACS analysis tools is ready as input for
Grace, formerly known as Xmgr. We use Grace, because it is very flexible, and it is also
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Your Own</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
-Sun 18 Jan 2009</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
+Sat 19 Jan 2013</B></td></tr></TABLE>
<HR>
<P><H2><A NAME="you">Your own System</A></H2>
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff