g_wham|weighted histogram analysis after umbrella sampling
xpm2ps|convert XPM (XPixelMap) file to postscript
g_sham|read/write xmgr and xvgr data sets
-g_spatial|calculates the spatial distribution function (more control than g_sdf)
-g_sdf|calculates the spatial distribution function (faster than g_spatial)
+g_spatial|calculates the spatial distribution function
g_select|selects groups of atoms based on flexible textual selections
g_tune_pme|time mdrun as a function of PME nodes to optimize settings
END
g_order|computes the order parameter per atom for carbon tails
g_principal|calculates axes of inertia for a group of atoms
g_rdf|calculates radial distribution functions
-g_sdf|calculates solvent distribution functions
g_sgangle|computes the angle and distance between two groups
g_sorient|analyzes solvent orientation around solutes
g_spol|analyzes solvent dipole orientation and polarization around solutes
+++ /dev/null
-.TH g_sdf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
-.SH NAME
-g_sdf - calculates the spatial distribution function (faster than g_spatial)
-
-.B VERSION 4.5
-.SH SYNOPSIS
-\f3g_sdf\fP
-.BI "\-f" " traj.xtc "
-.BI "\-n" " index.ndx "
-.BI "\-s" " topol.tpr "
-.BI "\-o" " gom_plt.dat "
-.BI "\-r" " refmol.gro "
-.BI "\-[no]h" ""
-.BI "\-[no]version" ""
-.BI "\-nice" " int "
-.BI "\-b" " time "
-.BI "\-e" " time "
-.BI "\-dt" " time "
-.BI "\-mode" " int "
-.BI "\-triangle" " vector "
-.BI "\-dtri" " vector "
-.BI "\-bin" " real "
-.BI "\-grid" " vector "
-.SH DESCRIPTION
-\&g_sdf calculates the spatial distribution function (SDF) of a set of atoms
-\&within a coordinate system defined by three atoms. There is single body,
-\&two body and three body SDF implemented (select with option \-mode).
-\&In the single body case the local coordinate system is defined by using
-\&a triple of atoms from one single molecule, for the two and three body case
-\&the configurations are dynamically searched complexes of two or three
-\&molecules (or residues) meeting certain distance consitions (see below).
-
-
-\&The program needs a trajectory, a GROMACS run input file and an index
-\&file to work.
-\&You have to setup 4 groups in the index file before using g_sdf:
-
-
-\&The first three groups are used to define the SDF coordinate system.
-\&The program will dynamically generate the atom triples according to
-\&the selected \-mode:
-\&In \-mode 1 the triples will be just the 1st, 2nd, 3rd, ... atoms from
-\&groups 1, 2 and 3. Hence the nth entries in groups 1, 2 and 3 must be from the
-\&same residue. In \-mode 2 the triples will be 1st, 2nd, 3rd, ... atoms from
-\&groups 1 and 2 (with the nth entries in groups 1 and 2 having the same res\-id).
-\&For each pair from groups 1 and 2 group 3 is searched for an atom meeting the
-\&distance conditions set with \-triangle and \-dtri relative to atoms 1 and 2. In
-\&\-mode 3 for each atom in group 1 group 2 is searched for an atom meeting the
-\&distance condition and if a pair is found group 3 is searched for an atom
-\&meeting the further conditions. The triple will only be used if all three atoms
-\&have different res\-id's.
-
-
-\&The local coordinate system is always defined using the following scheme:
-\&Atom 1 will be used as the point of origin for the SDF.
-\&Atom 1 and 2 will define the principle axis (Z) of the coordinate system.
-\&The other two axis will be defined inplane (Y) and normal (X) to the plane through
-\&Atoms 1, 2 and 3.
-\&The fourth group
-\&contains the atoms for which the SDF will be evaluated.
-
-
-\&For \-mode 2 and 3 you have to define the distance conditions for the
-\&2 resp. 3 molecule complexes to be searched for using \-triangle and \-dtri.
-
-
-\&The SDF will be sampled in cartesian coordinates.
-\&Use '\-grid x y z' to define the size of the SDF grid around the
-\&reference molecule.
-\&The Volume of the SDF grid will be V=x*y*z (nm3).
-\&Use \-bin to set the binwidth for grid.
-
-
-\&The output will be a binary 3D\-grid file (gom_plt.dat) in the .plt format that can be be
-\&read directly by gOpenMol.
-\&The option \-r will generate a .gro file with the reference molecule(s) transferred to
-\&the SDF coordinate system. Load this file into gOpenMol and display the
-\&SDF as a contour plot (see http://www.csc.fi/gopenmol/index.phtml for
-\&further documentation).
-
-
-\&For further information about SDF's have a look at: A. Vishnyakov, JPC A, 105,
-\&2001, 1702 and the references cited within.
-.SH FILES
-.BI "\-f" " traj.xtc"
-.B Input
- Trajectory: xtc trr trj gro g96 pdb cpt
-
-.BI "\-n" " index.ndx"
-.B Input
- Index file
-
-.BI "\-s" " topol.tpr"
-.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
-
-.BI "\-o" " gom_plt.dat"
-.B Output
- Generic data file
-
-.BI "\-r" " refmol.gro"
-.B Output, Opt.
- Structure file: gro g96 pdb etc.
-
-.SH OTHER OPTIONS
-.BI "\-[no]h" "no "
- Print help info and quit
-
-.BI "\-[no]version" "no "
- Print version info and quit
-
-.BI "\-nice" " int" " 19"
- Set the nicelevel
-
-.BI "\-b" " time" " 0 "
- First frame (ps) to read from trajectory
-
-.BI "\-e" " time" " 0 "
- Last frame (ps) to read from trajectory
-
-.BI "\-dt" " time" " 0 "
- Only use frame when t MOD dt = first time (ps)
-
-.BI "\-mode" " int" " 1"
- SDF in [1,2,3] particle mode
-
-.BI "\-triangle" " vector" " 0 0 0"
- r(1,3), r(2,3), r(1,2)
-
-.BI "\-dtri" " vector" " 0.03 0.03 0.03"
- dr(1,3), dr(2,3), dr(1,2)
-
-.BI "\-bin" " real" " 0.05 "
- Binwidth for the 3D\-grid (nm)
-
-.BI "\-grid" " vector" " 1 1 1"
- Size of the 3D\-grid (nm,nm,nm)
-
-.SH SEE ALSO
-.BR gromacs(7)
-
-More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
<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_sas.html>g_sas</a>
-<br><a href=online/g_sdf.html>g_sdf</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_sham.html>g_sham</a>
<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_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 (more control than g_sdf)</TD>
-<TR><TD><A HREF="online/g_sdf.html">g_sdf</A></TD><TD>calculates the spatial distribution function (faster than g_spatial)</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_tune_pme.html">g_tune_pme</A></TD><TD>time mdrun as a function of PME nodes to optimize settings</TD>
</TABLE>
<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_sdf.html">g_sdf</A></TD><TD>calculates solvent distribution functions</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>
+++ /dev/null
-<HTML>
-<HEAD>
-<TITLE>g_sdf</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_sdf</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>
-<HR>
-<H3>Description</H3>
-<p>
-g_sdf calculates the spatial distribution function (SDF) of a set of atoms
-within a coordinate system defined by three atoms. There is single body,
-two body and three body SDF implemented (select with option -mode).
-In the single body case the local coordinate system is defined by using
-a triple of atoms from one single molecule, for the two and three body case
-the configurations are dynamically searched complexes of two or three
-molecules (or residues) meeting certain distance consitions (see below).<p>
-The program needs a trajectory, a GROMACS run input file and an index
-file to work.
-You have to setup 4 groups in the index file before using g_sdf: <p>
-The first three groups are used to define the SDF coordinate system.
-The program will dynamically generate the atom triples according to
-the selected -mode:
-In -mode 1 the triples will be just the 1st, 2nd, 3rd, ... atoms from
-groups 1, 2 and 3. Hence the nth entries in groups 1, 2 and 3 must be from the
-same residue. In -mode 2 the triples will be 1st, 2nd, 3rd, ... atoms from
-groups 1 and 2 (with the nth entries in groups 1 and 2 having the same res-id).
-For each pair from groups 1 and 2 group 3 is searched for an atom meeting the
-distance conditions set with -triangle and -dtri relative to atoms 1 and 2. In
--mode 3 for each atom in group 1 group 2 is searched for an atom meeting the
-distance condition and if a pair is found group 3 is searched for an atom
-meeting the further conditions. The triple will only be used if all three atoms
-have different res-id's.<p>
-The local coordinate system is always defined using the following scheme:
-Atom 1 will be used as the point of origin for the SDF.
-Atom 1 and 2 will define the principle axis (Z) of the coordinate system.
-The other two axis will be defined inplane (Y) and normal (X) to the plane through
-Atoms 1, 2 and 3.
-The fourth group
-contains the atoms for which the SDF will be evaluated.<p>
-For -mode 2 and 3 you have to define the distance conditions for the
-2 resp. 3 molecule complexes to be searched for using -triangle and -dtri.<p>
-The SDF will be sampled in cartesian coordinates.
-Use '-grid x y z' to define the size of the SDF grid around the
-reference molecule.
-The Volume of the SDF grid will be V=x*y*z (nm^3).
-Use -bin to set the binwidth for grid.<p>
-The output will be a binary 3D-grid file (gom_plt.<a href="dat.html">dat</a>) in the .plt format that can be be
-read directly by gOpenMol.
-The option -r will generate a .<a href="gro.html">gro</a> file with the reference molecule(s) transferred to
-the SDF coordinate system. Load this file into gOpenMol and display the
-SDF as a contour plot (see http://www.csc.fi/gopenmol/index.phtml for
-further documentation). <p>
-For further information about SDF's have a look at: A. Vishnyakov, JPC A, 105,
-2001, 1702 and the references cited within.
-<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, 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>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> gom_plt.dat</a></tt> </TD><TD> Output </TD><TD> Generic data file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> refmol.gro</a></tt> </TD><TD> Output, Opt. </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>
-</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>-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>-mode</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> SDF in [1,2,3] particle mode </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-triangle</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> r(1,3), r(2,3), r(1,2) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dtri</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0.03 0.03 0.03</tt> </TD><TD> dr(1,3), dr(2,3), dr(1,2) </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> Binwidth for the 3D-grid (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-grid</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Size of the 3D-grid (nm,nm,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>
EXTRA_PROGRAMS = copyrgt \
options hrefify \
addquote compnl \
- gen_table ehole
+ gen_table ehole g_sdf
compnl_SOURCES = compnl.c
compnl_LDADD = ../mdlib/libmd@LIBSUFFIX@.la ../gmxlib/libgmx@LIBSUFFIX@.la
+g_sdg_SOURCES = gmx_sdf.c g_sdf.c
+
ehole_SOURCES = ehdata.c ehdata.h ehanal.c ehole.c
# Note: you don't have to list sources for "prog" if it is the single file prog.c
gmx_nmens.c gmx_order.c gmx_principal.c
gmx_polystat.c gmx_potential.c gmx_rama.c
gmx_rdf.c gmx_rms.c gmx_rmsdist.c gmx_rmsf.c
- gmx_rotacf.c gmx_saltbr.c gmx_sas.c gmx_sdf.c
+ gmx_rotacf.c gmx_saltbr.c gmx_sas.c
gmx_select.c
gmx_sgangle.c gmx_sorient.c gmx_spol.c gmx_tcaf.c
gmx_traj.c gmx_velacc.c gmx_helixorient.c
g_h2order g_hbond g_helix g_mindist g_msd g_morph g_nmeig
g_nmens g_order g_polystat g_potential g_rama g_rdf g_rms
g_rmsf g_rotacf g_saltbr g_sas g_select g_sgangle g_sham g_sorient
- g_spol g_sdf g_spatial g_tcaf g_traj g_tune_pme g_vanhove
+ g_spol g_spatial g_tcaf g_traj g_tune_pme g_vanhove
g_velacc g_clustsize g_mdmat g_wham g_sigeps g_bar
g_membed g_pme_error)
gmx_polystat.c gmx_potential.c gmx_rama.c \
gmx_rdf.c gmx_rms.c gmx_rmsdist.c gmx_rmsf.c \
gmx_rotacf.c gmx_rotmat.c gmx_saltbr.c gmx_sas.c \
- gmx_select.c gmx_sdf.c gmx_pme_error.c \
+ gmx_select.c gmx_pme_error.c \
gmx_sgangle.c gmx_sorient.c gmx_spol.c gmx_tcaf.c \
gmx_traj.c gmx_velacc.c gmx_helixorient.c \
gmx_clustsize.c gmx_mdmat.c gmx_wham.c eigio.h \
g_rotacf g_rotmat g_saltbr g_sas \
g_select g_sgangle \
g_sham g_sorient g_spol \
- g_sdf g_spatial g_pme_error \
+ g_spatial g_pme_error \
g_tcaf g_traj g_tune_pme \
g_vanhove g_velacc g_membed \
g_clustsize g_mdmat g_wham \
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff