man_MANS = \
anadock.1 g_cluster.1 g_filter.1 g_potential.1 \
- g_velacc.1 ngmx.1 cdist.1 g_clustsize.1 \
+ g_velacc.1 ngmx.1 g_clustsize.1 g_vanhove.1 \
g_gyrate.1 g_rama.1 g_wham.1 pdb2gmx.1 \
- disco.1 g_confrms.1 g_h2order.1 g_rdf.1 \
+ g_confrms.1 g_h2order.1 g_rdf.1 genrestr.1 \
genbox.1 protonate.1 do_dssp.1 g_covar.1 \
g_hbond.1 g_rms.1 genconf.1 tpbconv.1 \
editconf.1 g_density.1 g_helix.1 g_rmsdist.1 \
genion.1 trjcat.1 eneconv.1 g_dielectric.1 \
- g_lie.1 g_rmsf.1 genpr.1 trjconv.1 \
- ffscan.1 g_dih.1 g_mdmat.1 g_rotacf.1 \
+ g_lie.1 g_rmsf.1 trjconv.1 g_helixorient.1 \
+ g_dih.1 g_mdmat.1 g_rotacf.1 sigeps.1 \
gmxcheck.1 trjorder.1 g_anaeig.1 g_dipoles.1 \
g_mindist.1 g_saltbr.1 gmxdump.1 wheel.1 \
g_analyze.1 g_disre.1 g_morph.1 g_sas.1 \
make_ndx.1 xrama.1 g_bundle.1 g_enemat.1 \
g_nmens.1 g_tcaf.1 mdrun.1 g_chi.1 \
g_energy.1 g_order.1 g_traj.1 mk_angndx.1 \
- g_densmap.1 g_sham.1 make_edi.1
+ g_densmap.1 g_sham.1 make_edi.1 g_spol.1 \
+ g_spatial.1 g_sdf.1 g_rama.1 g_principal.1 \
+ g_polystat.1 g_nmtraj.1 g_current.1
EXTRA_DIST = ${man_MANS}
\ No newline at end of file
-.TH anadock 1 "Mon 29 Aug 2005"
+.TH anadock 1 "Mon 22 Sep 2008"
.SH NAME
anadock
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3anadock\fP
.BI "-f" " eiwit.pdb "
Log file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]free" " no"
+.BI "-[no]free" "no "
Use Free energy estimate from autodock for sorting the classes
-.BI "-[no]rms" " yes"
+.BI "-[no]rms" "yes "
Cluster on RMS or distance
-.BI "-cutoff" " real" " 0.2"
+.BI "-cutoff" " real" " 0.2 "
Maximum RMSD/distance for belonging to the same cluster
-.TH do_dssp 1 "Mon 29 Aug 2005"
+.TH do_dssp 1 "Mon 22 Sep 2008"
.SH NAME
do_dssp
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3do_dssp\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-sss" " string" " HEBT"
Secondary structures for structure count
-\- The program is very slow
-
-.TH editconf 1 "Mon 29 Aug 2005"
+.TH editconf 1 "Mon 22 Sep 2008"
.SH NAME
editconf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3editconf\fP
.BI "-f" " conf.gro "
Option
.B -bt
determines the box type:
-.B tric
+.B triclinic
is a
triclinic box,
.B cubic
-is a cubic box,
+is a rectangular box with all sides equal
+
.B dodecahedron
-is
-a rhombic dodecahedron and
+represents a rhombic dodecahedron and
.B octahedron
is a truncated octahedron.
The last two are special cases of a triclinic box.
.B -box
requires only
one value for a cubic box, dodecahedron and a truncated octahedron.
+
+
+
With
.B -d
-and
-.B tric
-the size of the system in the x, y
+and a
+.B triclinic
+box the size of the system in the x, y
and z directions is used. With
.B -d
and
.B dodecahedron
or
.B octahedron
-the diameter of the system
-is used, which is the largest distance between two atoms.
+boxes, the dimensions are set
+to the diameter of the system (largest distance between atoms) plus twice
+the specified distance.
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " out.gro"
.B Output, Opt.
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-mead" " mead.pqr"
.B Output, Opt.
Generic data file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]ndef" " no"
+.BI "-[no]ndef" "no "
Choose output from default index groups
-.BI "-bt" " enum" " tric"
+.BI "-bt" " enum" " triclinic"
Box type for -box and -d:
-.B tric
+.B triclinic
,
.B cubic
,
.BI "-angles" " vector" " 90 90 90"
Angles between the box vectors (bc,ac,ab)
-.BI "-d" " real" " 0"
+.BI "-d" " real" " 0 "
Distance between the solute and the box
-.BI "-[no]c" " no"
+.BI "-[no]c" "no "
Center molecule in box (implied by -box and -d)
.BI "-center" " vector" " 0 0 0"
.BI "-rotate" " vector" " 0 0 0"
Rotation around the X, Y and Z axes in degrees
-.BI "-[no]princ" " no"
+.BI "-[no]princ" "no "
Orient molecule(s) along their principal axes
.BI "-scale" " vector" " 1 1 1"
Scaling factor
-.BI "-density" " real" " 1000"
+.BI "-density" " real" " 1000 "
Density (g/l) of the output box achieved by scaling
-.BI "-[no]vol" " yes"
+.BI "-[no]vol" "yes "
Compute and print volume of the box
-.BI "-[no]pbc" " no"
+.BI "-[no]pbc" "no "
Remove the periodicity (make molecule whole again)
-.BI "-[no]grasp" " no"
+.BI "-[no]grasp" "no "
Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field
-.BI "-rvdw" " real" " 0.12"
+.BI "-rvdw" " real" " 0.12 "
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
-.BI "-sig56" " real" " 0"
+.BI "-sig56" " real" " 0 "
Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
-.BI "-[no]vdwread" " no"
+.BI "-[no]vdwread" "no "
Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
-.BI "-[no]atom" " no"
+.BI "-[no]atom" "no "
Force B-factor attachment per atom
-.BI "-[no]legend" " no"
+.BI "-[no]legend" "no "
Make B-factor legend
.BI "-label" " string" " A"
Add chain label for all residues
+.SH KNOWN PROBLEMS
\- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv
-.TH eneconv 1 "Mon 29 Aug 2005"
+.TH eneconv 1 "Mon 22 Sep 2008"
.SH NAME
eneconv
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3eneconv\fP
.BI "-f" " ener.edr "
.SH FILES
.BI "-f" " ener.edr"
.B Input, Mult.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-o" " fixed.edr"
.B Output
- Generic energy: edr ene
+ Energy file: edr ene
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " real" " -1"
+.BI "-b" " real" " -1 "
First time to use
-.BI "-e" " real" " -1"
+.BI "-e" " real" " -1 "
Last time to use
-.BI "-dt" " real" " 0"
+.BI "-dt" " real" " 0 "
Only write out frame when t MOD dt = offset
-.BI "-offset" " real" " 0"
+.BI "-offset" " real" " 0 "
Time offset for -dt option
-.BI "-[no]settime" " no"
+.BI "-[no]settime" "no "
Change starting time interactively
-.BI "-[no]sort" " yes"
+.BI "-[no]sort" "yes "
Sort energy files (not frames)
-.BI "-scalefac" " real" " 1"
+.BI "-scalefac" " real" " 1 "
Multiply energy component by this factor
-.BI "-[no]error" " yes"
+.BI "-[no]error" "yes "
Stop on errors in the file
+.SH KNOWN PROBLEMS
\- When combining trajectories the sigma and E2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way.
-.TH g_anaeig 1 "Mon 29 Aug 2005"
+.TH g_anaeig 1 "Mon 22 Sep 2008"
.SH NAME
g_anaeig
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_anaeig\fP
.BI "-v" " eigenvec.trr "
.BI "-max" " real "
.BI "-nframes" " int "
.BI "-[no]split" ""
+.BI "-[no]entropy" ""
+.BI "-temp" " real "
+.BI "-nevskip" " int "
.SH DESCRIPTION
.B g_anaeig
root of the fluctuations. The normalized overlap is the most useful
number, it is 1 for identical matrices and 0 when the sampled
subspaces are orthogonal.
+
+
+When the
+.B -entropy
+flag is given an entropy estimate will be
+computed based on the Quasiharmonic approach and based on
+Schlitter's formula.
.SH FILES
.BI "-v" " eigenvec.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-v2" " eigenvec2.trr"
.B Input, Opt.
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-3d" " 3dproj.pdb"
.B Output, Opt.
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-filt" " filtered.xtc"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-extr" " extreme.pdb"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-over" " overlap.xvg"
.B Output, Opt.
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-first" " int" " 1"
.BI "-skip" " int" " 1"
Only analyse every nr-th frame
-.BI "-max" " real" " 0"
+.BI "-max" " real" " 0 "
Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes
.BI "-nframes" " int" " 2"
Number of frames for the extremes output
-.BI "-[no]split" " no"
+.BI "-[no]split" "no "
Split eigenvector projections where time is zero
+.BI "-[no]entropy" "no "
+ Compute entropy according to the Quasiharmonic formula or Schlitter's method.
+
+.BI "-temp" " real" " 298.15"
+ Temperature for entropy calculations
+
+.BI "-nevskip" " int" " 6"
+ 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.
+
-.TH g_analyze 1 "Mon 29 Aug 2005"
+.TH g_analyze 1 "Mon 22 Sep 2008"
.SH NAME
g_analyze
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_analyze\fP
.BI "-f" " graph.xvg "
.BI "-[no]integrate" ""
.BI "-aver_start" " real "
.BI "-[no]xydy" ""
+.BI "-[no]regression" ""
+.BI "-[no]luzar" ""
+.BI "-temp" " real "
+.BI "-fitstart" " real "
+.BI "-smooth" " real "
.BI "-filter" " real "
.BI "-[no]power" ""
.BI "-[no]subav" ""
.B -cc
plots the resemblance of set i with a cosine of
i/2 periods. The formula is:
-2 (int0-T y(t) cos(pi t/i) dt)2 / int0-T y(t) y(t) dt
+2 (int0-T y(t) cos(i pi t) dt)2 / int0-T y(t) y(t) dt
This is useful for principal components obtained from covariance
analysis, since the principal components of random diffusion are
of 0.79 and 0.33 respectively.
+Option
+.B -g
+fits the data to the function given with option
+
+.B -fitfn
+.
+
+
Option
.B -power
fits the data to b ta, which is accomplished
by fitting to a t + b on log-log scale. All points after the first
zero or negative value are ignored.
+
+Option
+.B -luzar
+performs a Luzar & Chandler kinetics analysis
+on output from
+.B g_hbond
+. The input file can be taken directly
+from
+.B g_hbond -ac
+, and then the same result should be produced.
.SH FILES
.BI "-f" " graph.xvg"
.B Input
Log file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]time" " yes"
+.BI "-[no]time" "yes "
Expect a time in the input
-.BI "-b" " real" " -1"
+.BI "-b" " real" " -1 "
First time to read from set
-.BI "-e" " real" " -1"
+.BI "-e" " real" " -1 "
Last time to read from set
.BI "-n" " int" " 1"
Read sets seperated by &
-.BI "-[no]d" " no"
+.BI "-[no]d" "no "
Use the derivative
-.BI "-bw" " real" " 0.1"
+.BI "-bw" " real" " 0.1 "
Binwidth for the distribution
.BI "-errbar" " enum" " none"
.B 90
-.BI "-[no]integrate" " no"
+.BI "-[no]integrate" "no "
Integrate data function(s) numerically using trapezium rule
-.BI "-aver_start" " real" " 0"
+.BI "-aver_start" " real" " 0 "
Start averaging the integral from here
-.BI "-[no]xydy" " no"
+.BI "-[no]xydy" "no "
Interpret second data set as error in the y values for integrating
-.BI "-filter" " real" " 0"
+.BI "-[no]regression" "no "
+ Perform a linear regression analysis on the data
+
+.BI "-[no]luzar" "no "
+ Do a Luzar and Chandler analysis on a correlation function and related as produced by g_hbond. When in addition the -xydy flag is given the second and fourth column will be interpreted as errors in c(t) and n(t).
+
+.BI "-temp" " real" " 298.15"
+ Temperature for the Luzar hydrogen bonding kinetics analysis
+
+.BI "-fitstart" " real" " 1 "
+ 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
+
+.BI "-smooth" " real" " -1 "
+ If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)
+
+.BI "-filter" " real" " 0 "
Print the high-frequency fluctuation after filtering with a cosine filter of length
-.BI "-[no]power" " no"
+.BI "-[no]power" "no "
Fit data to: b ta
-.BI "-[no]subav" " yes"
+.BI "-[no]subav" "yes "
Subtract the average before autocorrelating
-.BI "-[no]oneacf" " no"
+.BI "-[no]oneacf" "no "
Calculate one ACF over all sets
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_angle 1 "Mon 29 Aug 2005"
+.TH g_angle 1 "Mon 22 Sep 2008"
.SH NAME
g_angle
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_angle\fP
.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
.BI "-n" " angle.ndx "
.BI "-od" " angdist.xvg "
.BI "-ov" " angaver.xvg "
.BI "-type" " enum "
.BI "-[no]all" ""
.BI "-binwidth" " real "
+.BI "-[no]periodic" ""
.BI "-[no]chandler" ""
.BI "-[no]avercorr" ""
.BI "-acflen" " int "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-s" " topol.tpr"
-.B Input
- Generic run input: tpr tpb tpa xml
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " angle.ndx"
.B Input
Trajectory in portable xdr format
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-type" " enum" " angle"
.B ryckaert-bellemans
-.BI "-[no]all" " no"
+.BI "-[no]all" "no "
Plot all angles separately in the averages file, in the order of appearance in the index file.
-.BI "-binwidth" " real" " 1"
+.BI "-binwidth" " real" " 1 "
binwidth (degrees) for calculating the distribution
-.BI "-[no]chandler" " no"
+.BI "-[no]periodic" "yes "
+ Print dihedral angles modulo 360 degrees
+
+.BI "-[no]chandler" "no "
Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi -60 || phi 60.
-.BI "-[no]avercorr" " no"
+.BI "-[no]avercorr" "no "
Average the correlation functions for the individual angles/dihedrals
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
+.SH KNOWN PROBLEMS
\- Counting transitions only works for dihedrals with multiplicity 3
-.TH g_bond 1 "Mon 29 Aug 2005"
+.TH g_bond 1 "Mon 22 Sep 2008"
.SH NAME
g_bond
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_bond\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-o" " bonds.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-blen" " real" " -1"
+.BI "-blen" " real" " -1 "
Bond length. By default length of first bond
-.BI "-tol" " real" " 0.1"
+.BI "-tol" " real" " 0.1 "
Half width of distribution as fraction of blen
-.BI "-[no]aver" " yes"
+.BI "-[no]aver" "yes "
Average bond length distributions
-.BI "-[no]averdist" " yes"
+.BI "-[no]averdist" "yes "
Average distances (turns on -d)
+.SH KNOWN PROBLEMS
\- It should be possible to get bond information from the topology.
-.TH g_bundle 1 "Mon 29 Aug 2005"
+.TH g_bundle 1 "Mon 22 Sep 2008"
.SH NAME
g_bundle
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_bundle\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Protein data bank file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-na" " int" " 0"
Number of axes
-.BI "-[no]z" " no"
+.BI "-[no]z" "no "
Use the Z-axis as reference iso the average axis
-.TH g_chi 1 "Mon 29 Aug 2005"
+.TH g_chi 1 "Mon 22 Sep 2008"
.SH NAME
g_chi
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_chi\fP
.BI "-s" " conf.gro "
.BI "-[no]omega" ""
.BI "-[no]rama" ""
.BI "-[no]viol" ""
+.BI "-[no]periodic" ""
.BI "-[no]all" ""
.BI "-[no]rad" ""
.BI "-[no]shift" ""
.SH FILES
.BI "-s" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-o" " order.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-r0" " int" " 1"
starting residue
-.BI "-[no]phi" " no"
+.BI "-[no]phi" "no "
Output for Phi dihedral angles
-.BI "-[no]psi" " no"
+.BI "-[no]psi" "no "
Output for Psi dihedral angles
-.BI "-[no]omega" " no"
+.BI "-[no]omega" "no "
Output for Omega dihedrals (peptide bonds)
-.BI "-[no]rama" " no"
+.BI "-[no]rama" "no "
Generate Phi/Psi and Chi1/Chi2 ramachandran plots
-.BI "-[no]viol" " no"
+.BI "-[no]viol" "no "
Write a file that gives 0 or 1 for violated Ramachandran angles
-.BI "-[no]all" " no"
+.BI "-[no]periodic" "yes "
+ Print dihedral angles modulo 360 degrees
+
+.BI "-[no]all" "no "
Output separate files for every dihedral.
-.BI "-[no]rad" " no"
+.BI "-[no]rad" "no "
in angle vs time files, use radians rather than degrees.
-.BI "-[no]shift" " no"
+.BI "-[no]shift" "no "
Compute chemical shifts from Phi/Psi angles
.BI "-binwidth" " int" " 1"
bin width for histograms (degrees)
-.BI "-core_rotamer" " real" " 0.5"
+.BI "-core_rotamer" " real" " 0.5 "
only the central -core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)
.BI "-maxchi" " enum" " 0"
.B 6
-.BI "-[no]normhisto" " yes"
+.BI "-[no]normhisto" "yes "
Normalize histograms
-.BI "-[no]ramomega" " no"
+.BI "-[no]ramomega" "no "
compute average omega as a function of phi/psi and plot it in an xpm plot
-.BI "-bfact" " real" " -1"
+.BI "-bfact" " real" " -1 "
B-factor value for pdb file for atoms with no calculated dihedral order parameter
-.BI "-[no]chi_prod" " no"
+.BI "-[no]chi_prod" "no "
compute a single cumulative rotamer for each residue
-.BI "-[no]HChi" " no"
+.BI "-[no]HChi" "no "
Include dihedrals to sidechain hydrogens
-.BI "-bmax" " real" " 0"
+.BI "-bmax" " real" " 0 "
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.
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
+.SH KNOWN PROBLEMS
\- 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.
\- 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 g_rama.
-.TH g_cluster 1 "Mon 29 Aug 2005"
+.TH g_cluster 1 "Mon 22 Sep 2008"
.SH NAME
g_cluster
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_cluster\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-cl" " clusters.pdb"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]dista" " no"
+.BI "-[no]dista" "no "
Use RMSD of distances instead of RMS deviation
.BI "-nlevels" " int" " 40"
Discretize RMSD matrix in levels
-.BI "-cutoff" " real" " 0.1"
+.BI "-cutoff" " real" " 0.1 "
RMSD cut-off (nm) for two structures to be neighbor
-.BI "-[no]fit" " yes"
+.BI "-[no]fit" "yes "
Use least squares fitting before RMSD calculation
-.BI "-max" " real" " -1"
+.BI "-max" " real" " -1 "
Maximum level in RMSD matrix
.BI "-skip" " int" " 1"
Only analyze every nr-th frame
-.BI "-[no]av" " no"
+.BI "-[no]av" "no "
Write average iso middle structure for each cluster
.BI "-wcl" " int" " 0"
.BI "-nst" " int" " 1"
Only write all structures if more than per cluster
-.BI "-rmsmin" " real" " 0"
+.BI "-rmsmin" " real" " 0 "
minimum rms difference with rest of cluster for writing structures
.BI "-method" " enum" " linkage"
.BI "-minstruct" " int" " 1"
Minimum number of structures in cluster for coloring in the xpm file
-.BI "-[no]binary" " no"
+.BI "-[no]binary" "no "
Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff
.BI "-M" " int" " 10"
.BI "-niter" " int" " 10000"
Number of iterations for MC
-.BI "-kT" " real" " 0.001"
+.BI "-kT" " real" " 0.001 "
Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps)
-.TH g_clustsize 1 "Mon 29 Aug 2005"
+.TH g_clustsize 1 "Mon 22 Sep 2008"
.SH NAME
g_clustsize
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_clustsize\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-cut" " real" " 0.35"
+.BI "-cut" " real" " 0.35 "
Largest distance (nm) to be considered in a cluster
-.BI "-[no]mol" " no"
+.BI "-[no]mol" "no "
Cluster molecules rather than atoms (needs tpr file)
-.BI "-[no]pbc" " yes"
+.BI "-[no]pbc" "yes "
Use periodic boundary conditions
.BI "-nskip" " int" " 0"
-.TH g_confrms 1 "Mon 29 Aug 2005"
+.TH g_confrms 1 "Mon 22 Sep 2008"
.SH NAME
g_confrms
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_confrms\fP
.BI "-f1" " conf1.gro "
.BI "-[no]pbc" ""
.BI "-[no]fit" ""
.BI "-[no]name" ""
+.BI "-[no]label" ""
.BI "-[no]bfac" ""
.SH DESCRIPTION
g_confrms computes the root mean square deviation (RMSD) of two
.SH FILES
.BI "-f1" " conf1.gro"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-f2" " conf2.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " fit.pdb"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-n1" " fit1.ndx"
.B Input, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]one" " no"
+.BI "-[no]one" "no "
Only write the fitted structure to file
-.BI "-[no]mw" " yes"
+.BI "-[no]mw" "yes "
Mass-weighted fitting and RMSD
-.BI "-[no]pbc" " no"
+.BI "-[no]pbc" "no "
Try to make molecules whole again
-.BI "-[no]fit" " yes"
+.BI "-[no]fit" "yes "
Do least squares superposition of the target structure to the reference
-.BI "-[no]name" " no"
+.BI "-[no]name" "no "
Only compare matching atom names
-.BI "-[no]bfac" " no"
+.BI "-[no]label" "no "
+ Added chain labels A for first and B for second structure
+
+.BI "-[no]bfac" "no "
Output B-factors from atomic MSD values
-.TH g_covar 1 "Mon 29 Aug 2005"
+.TH g_covar 1 "Mon 22 Sep 2008"
.SH NAME
g_covar
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_covar\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-v" " eigenvec.trr"
.B Output
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-av" " average.pdb"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-l" " covar.log"
.B Output
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]fit" " yes"
+.BI "-[no]fit" "yes "
Fit to a reference structure
-.BI "-[no]ref" " no"
+.BI "-[no]ref" "no "
Use the deviation from the conformation in the structure file instead of from the average
-.BI "-[no]mwa" " no"
+.BI "-[no]mwa" "no "
Mass-weighted covariance analysis
.BI "-last" " int" " -1"
Last eigenvector to write away (-1 is till the last)
-.BI "-[no]pbc" " yes"
+.BI "-[no]pbc" "yes "
Apply corrections for periodic boundary conditions
-.TH g_density 1 "Mon 29 Aug 2005"
+.TH g_density 1 "Mon 22 Sep 2008"
.SH NAME
g_density
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_density\fP
.BI "-f" " traj.xtc "
.BI "-[no]xvgr" ""
.BI "-d" " string "
.BI "-sl" " int "
-.BI "-[no]number" ""
-.BI "-[no]ed" ""
-.BI "-[no]count" ""
+.BI "-dens" " enum "
.BI "-ng" " int "
.BI "-[no]symm" ""
.BI "-[no]center" ""
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-ei" " electrons.dat"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-d" " string" " Z"
Take the normal on the membrane in direction X, Y or Z.
-.BI "-sl" " int" " 10"
+.BI "-sl" " int" " 50"
Divide the box in nr slices.
-.BI "-[no]number" " no"
- Calculate number density instead of mass density. Hydrogens are not counted!
+.BI "-dens" " enum" " mass"
+ Density:
+.B mass
+,
+.B number
+,
+.B charge
+or
+.B electron
-.BI "-[no]ed" " no"
- Calculate electron density instead of mass density
-.BI "-[no]count" " no"
- Only count atoms in slices, no densities. Hydrogens are not counted
-
-.BI "-ng" " int" " 0"
+.BI "-ng" " int" " 1"
Number of groups to compute densities of
-.BI "-[no]symm" " no"
+.BI "-[no]symm" "no "
Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
-.BI "-[no]center" " no"
+.BI "-[no]center" "no "
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.
+.SH KNOWN PROBLEMS
\- When calculating electron densities, atomnames are used instead of types. This is bad.
-\- When calculating number densities, atoms with names that start with H are not counted. This may be surprising if you use hydrogens with names like OP3.
-
-.TH g_densmap 1 "Mon 29 Aug 2005"
+.TH g_densmap 1 "Mon 22 Sep 2008"
.SH NAME
g_densmap
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_densmap\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-bin" " real "
-.BI "-nx" " int "
-.BI "-nz" " int "
+.BI "-aver" " enum "
+.BI "-xmin" " real "
+.BI "-xmax" " real "
+.BI "-n1" " int "
+.BI "-n2" " int "
.BI "-amax" " real "
.BI "-rmax" " real "
.BI "-[no]mirror" ""
+.BI "-unit" " enum "
+.BI "-dmin" " real "
.BI "-dmax" " real "
.SH DESCRIPTION
g_densmap computes 2D number-density maps.
The default analysis is a 2-D number-density map for a selected
-group of atoms in the x-z plane. The grid spacing is set with the option
-
+group of atoms in the x-y plane.
+The averaging direction can be changed with the option
+.B -aver
+.
+When
+.B -xmin
+and/or
+.B -xmax
+are set only atoms that are
+within the limit(s) in the averaging direction are taken into account.
+The grid spacing is set with the option
.B -bin
-. When
-.B -nx
+.
+When
+.B -n1
or
-.B -nz
+.B -n2
is non-zero, the grid
-size is set by this option. Box size fluctuations are properly taken
-into account.
+size is set by this option.
+Box size fluctuations are properly taken into account.
+The normalization of the output is set with the
+.B -unit
+option.
+The default produces a true number density. Unit
+.B nm-2
+leaves out
+the normalization for the averaging or the angular direction.
+Option
+.B count
+produces the count for each grid cell.
When you do not want the scale in the output to go
from zero to the maximum density, you can set the maximum
with the option
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-bin" " real" " 0.02"
- Grid size
+.BI "-bin" " real" " 0.02 "
+ Grid size (nm)
+
+.BI "-aver" " enum" " z"
+ The direction to average over:
+.B z
+,
+.B y
+or
+.B x
+
-.BI "-nx" " int" " 0"
- Number of grid cells in x direction
+.BI "-xmin" " real" " -1 "
+ Minimum coordinate for averaging
-.BI "-nz" " int" " 0"
- Number of grid cells in z direction
+.BI "-xmax" " real" " -1 "
+ Maximum coordinate for averaging
-.BI "-amax" " real" " 0"
+.BI "-n1" " int" " 0"
+ Number of grid cells in the first direction
+
+.BI "-n2" " int" " 0"
+ Number of grid cells in the second direction
+
+.BI "-amax" " real" " 0 "
Maximum axial distance from the center
-.BI "-rmax" " real" " 0"
+.BI "-rmax" " real" " 0 "
Maximum radial distance
-.BI "-[no]mirror" " no"
+.BI "-[no]mirror" "no "
Add the mirror image below the axial axis
-.BI "-dmax" " real" " 0"
- Maximum density (0 means calculate it)
+.BI "-unit" " enum" " nm-3"
+ Unit for the output:
+.B nm-3
+,
+.B nm-2
+or
+.B count
+
+
+.BI "-dmin" " real" " 0 "
+ Minimum density in output
+
+.BI "-dmax" " real" " 0 "
+ Maximum density in output (0 means calculate it)
-.TH g_dielectric 1 "Mon 29 Aug 2005"
+.TH g_dielectric 1 "Mon 22 Sep 2008"
.SH NAME
g_dielectric
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dielectric\fP
-.BI "-f" " Mtot.xvg "
+.BI "-f" " dipcorr.xvg "
.BI "-d" " deriv.xvg "
.BI "-o" " epsw.xvg "
.BI "-c" " cole.xvg "
For a pure exponential relaxation (Debye relaxation) the latter
plot should be one half of a circle
.SH FILES
-.BI "-f" " Mtot.xvg"
+.BI "-f" " dipcorr.xvg"
.B Input
xvgr/xmgr file
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]fft" " no"
+.BI "-[no]fft" "no "
use fast fourier transform for correlation function
-.BI "-[no]x1" " yes"
+.BI "-[no]x1" "yes "
use first column as X axis rather than first data set
-.BI "-eint" " real" " 5"
+.BI "-eint" " real" " 5 "
Time were to end the integration of the data and start to use the fit
-.BI "-bfit" " real" " 5"
+.BI "-bfit" " real" " 5 "
Begin time of fit
-.BI "-efit" " real" " 500"
+.BI "-efit" " real" " 500 "
End time of fit
-.BI "-tail" " real" " 500"
+.BI "-tail" " real" " 500 "
Length of function including data and tail from fit
-.BI "-A" " real" " 0.5"
+.BI "-A" " real" " 0.5 "
Start value for fit parameter A
-.BI "-tau1" " real" " 10"
+.BI "-tau1" " real" " 10 "
Start value for fit parameter tau1
-.BI "-tau2" " real" " 1"
+.BI "-tau2" " real" " 1 "
Start value for fit parameter tau2
-.BI "-eps0" " real" " 80"
+.BI "-eps0" " real" " 80 "
Epsilon 0 of your liquid
-.BI "-epsRF" " real" " 78.5"
+.BI "-epsRF" " real" " 78.5 "
Epsilon of the reaction field used in your simulation. A value of 0 means infinity.
.BI "-fix" " int" " 0"
-.TH g_dih 1 "Mon 29 Aug 2005"
+.TH g_dih 1 "Mon 22 Sep 2008"
.SH NAME
g_dih
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dih\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " hello.out"
.B Output
Generic output file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]sa" " no"
+.BI "-[no]sa" "no "
Perform cluster analysis in dihedral space instead of analysing dihedral transitions.
.BI "-mult" " int" " -1"
-.TH g_dipoles 1 "Mon 29 Aug 2005"
+.TH g_dipoles 1 "Mon 22 Sep 2008"
.SH NAME
g_dipoles
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dipoles\fP
.BI "-enx" " ener.edr "
.BI "-adip" " adip.xvg "
.BI "-dip3d" " dip3d.xvg "
.BI "-cos" " cosaver.xvg "
+.BI "-cmap" " cmap.xpm "
.BI "-q" " quadrupole.xvg "
.BI "-slab" " slab.xvg "
.BI "-[no]h" ""
.BI "-epsilonRF" " real "
.BI "-skip" " int "
.BI "-temp" " real "
-.BI "-[no]avercorr" ""
+.BI "-corr" " enum "
.BI "-[no]pairs" ""
+.BI "-ncos" " int "
.BI "-axis" " string "
.BI "-sl" " int "
.BI "-gkratom" " int "
+.BI "-gkratom2" " int "
+.BI "-rcmax" " real "
+.BI "-[no]phi" ""
+.BI "-nlevels" " int "
+.BI "-ndegrees" " int "
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.BI "-P" " enum "
.SH DESCRIPTION
g_dipoles 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.
The file Mtot.xvg contains the total dipole moment of a frame, the
The mu_max is used as the highest value in the distribution graph.
-Furthermore the dipole autocorrelation function will be computed, when
-option -c is used. It can be averaged over all molecules,
-or (with option -avercorr) it can be computed as the autocorrelation
-of the total dipole moment of the simulation box.
+Furthermore the dipole autocorrelation function will be computed when
+option -corr is used. The output file name is given with the
+.B -c
-
-At the moment the dielectric constant is calculated only correct if
-a rectangular or cubic simulation box is used.
+option.
+The correlation functions can be averaged over all molecules
+(
+.B mol
+), plotted per molecule seperately (
+.B molsep
+)
+or it can be computed over the total dipole moment of the simulation box
+(
+.B total
+).
Option
EXAMPLES
-g_dipoles -P1 -n mols -o dip_sqr -mu 2.273 -mumax 5.0
--nofft
+g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft
This will calculate the autocorrelation function of the molecular
.SH FILES
.BI "-enx" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
+.BI "-cmap" " cmap.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
.BI "-q" " quadrupole.xvg"
.B Output, Opt.
xvgr/xmgr file
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-mu" " real" " -1"
+.BI "-mu" " real" " -1 "
dipole of a single molecule (in Debye)
-.BI "-mumax" " real" " 5"
+.BI "-mumax" " real" " 5 "
max dipole in Debye (for histrogram)
-.BI "-epsilonRF" " real" " 0"
+.BI "-epsilonRF" " real" " 0 "
epsilon of the reaction field used during the simulation, needed for dieclectric constant calculation. WARNING: 0.0 means infinity (default)
.BI "-skip" " int" " 0"
Skip steps in the output (but not in the computations)
-.BI "-temp" " real" " 300"
- average temperature of the simulation (needed for dielectric constant calculation)
+.BI "-temp" " real" " 300 "
+ Average temperature of the simulation (needed for dielectric constant calculation)
+
+.BI "-corr" " enum" " none"
+ Correlation function to calculate:
+.B none
+,
+.B mol
+,
+.B molsep
+or
+.B total
-.BI "-[no]avercorr" " no"
- calculate AC function of average dipole moment of the simulation box rather than average of AC function per molecule
-.BI "-[no]pairs" " yes"
+.BI "-[no]pairs" "yes "
Calculate |cos theta| between all pairs of molecules. May be slow
+.BI "-ncos" " int" " 1"
+ 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.
+
.BI "-axis" " string" " Z"
Take the normal on the computational box in direction X, Y or Z.
.BI "-gkratom" " int" " 0"
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
+.BI "-gkratom2" " int" " 0"
+ Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules
+
+.BI "-rcmax" " real" " 0 "
+ Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used.
+
+.BI "-[no]phi" "no "
+ Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the xpm file from the -cmap option. By default the cosine of the angle between the dipoles is plotted.
+
+.BI "-nlevels" " int" " 20"
+ Number of colors in the cmap output
+
+.BI "-ndegrees" " int" " 90"
+ Number of divisions on the y-axis in the camp output (for 180 degrees)
+
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_disre 1 "Mon 29 Aug 2005"
+.TH g_disre 1 "Mon 22 Sep 2008"
.SH NAME
g_disre
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_disre\fP
.BI "-s" " topol.tpr "
.BI "-n" " viol.ndx "
.BI "-q" " viol.pdb "
.BI "-c" " clust.ndx "
+.BI "-x" " matrix.xpm "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
.BI "-ntop" " int "
+.BI "-maxdr" " real "
+.BI "-nlevels" " int "
+.BI "-[no]third" ""
.SH DESCRIPTION
g_disre computes violations of distance restraints.
If necessary all protons can be added to a protein molecule
using the protonate program.
-The program allways
+The program always
computes the instantaneous violations rather than time-averaged,
because this analysis is done from a trajectory file afterwards
it does not make sense to use time averaging. However,
option is given, an index file will be read
containing the frames in your trajectory corresponding to the clusters
(defined in another manner) that you want to analyze. For these clusters
-the program will compute average violations using the thisd power
+the program will compute average violations using the third power
averaging algorithm and print them in the log file.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-ds" " drsum.xvg"
.B Output
.B Input, Opt.
Index file
+.BI "-x" " matrix.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-ntop" " int" " 0"
Number of large violations that are stored in the log file every step
+.BI "-maxdr" " real" " 0 "
+ Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data.
+
+.BI "-nlevels" " int" " 20"
+ Number of levels in the matrix output
+
+.BI "-[no]third" "yes "
+ Use inverse third power averaging or linear for matrix output
+
-.TH g_dist 1 "Mon 29 Aug 2005"
+.TH g_dist 1 "Mon 22 Sep 2008"
.SH NAME
g_dist
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dist\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-o" " dist.xvg "
+.BI "-lt" " lifetime.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
closer than a certain distance to the center of mass of group 1.
+With options
+.B -lt
+and
+.B -dist
+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.
+
+
Other programs that calculate distances are
.B g_mindist
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
+.BI "-lt" " lifetime.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-dist" " real" " 0"
+.BI "-dist" " real" " 0 "
Print all atoms in group 2 closer than dist to the center of mass of group 1
-.TH g_dyndom 1 "Mon 29 Aug 2005"
+.TH g_dyndom 1 "Mon 22 Sep 2008"
.SH NAME
g_dyndom
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dyndom\fP
.BI "-f" " dyndom.pdb "
.BI "-tail" " vector "
.SH DESCRIPTION
g_dyndom reads a pdb file output from DynDom
-http://md.chem.rug.nl/~steve/DynDom/dyndom.home.html
+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
.BI "-o" " rotated.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-n" " domains.ndx"
.B Input
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-firstangle" " real" " 0"
+.BI "-firstangle" " real" " 0 "
Angle of rotation about rotation vector
-.BI "-lastangle" " real" " 0"
+.BI "-lastangle" " real" " 0 "
Angle of rotation about rotation vector
.BI "-nframe" " int" " 11"
Number of steps on the pathway
-.BI "-maxangle" " real" " 0"
+.BI "-maxangle" " real" " 0 "
DymDom dtermined angle of rotation about rotation vector
-.BI "-trans" " real" " 0"
+.BI "-trans" " real" " 0 "
Translation (Aangstroem) along rotation vector (see DynDom info file)
.BI "-head" " vector" " 0 0 0"
-.TH g_enemat 1 "Mon 29 Aug 2005"
+.TH g_enemat 1 "Mon 22 Sep 2008"
.SH NAME
g_enemat
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_enemat\fP
.BI "-f" " ener.edr "
.SH FILES
.BI "-f" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-groups" " groups.dat"
.B Input
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]sum" " no"
+.BI "-[no]sum" "no "
Sum the energy terms selected rather than display them all
.BI "-skip" " int" " 0"
Skip number of frames between data points
-.BI "-[no]mean" " yes"
+.BI "-[no]mean" "yes "
with -groups extracts matrix of mean energies in stead of matrix for each timestep
.BI "-nlevels" " int" " 20"
number of levels for matrix colors
-.BI "-max" " real" " 1e+20"
+.BI "-max" " real" " 1e+20 "
max value for energies
.BI "-min" " real" " -1e+20"
min value for energies
-.BI "-[no]coul" " yes"
+.BI "-[no]coul" "yes "
extract Coulomb SR energies
-.BI "-[no]coulr" " no"
+.BI "-[no]coulr" "no "
extract Coulomb LR energies
-.BI "-[no]coul14" " no"
+.BI "-[no]coul14" "no "
extract Coulomb 1-4 energies
-.BI "-[no]lj" " yes"
+.BI "-[no]lj" "yes "
extract Lennard-Jones SR energies
-.BI "-[no]lj" " no"
+.BI "-[no]lj" "no "
extract Lennard-Jones LR energies
-.BI "-[no]lj14" " no"
+.BI "-[no]lj14" "no "
extract Lennard-Jones 1-4 energies
-.BI "-[no]bhamsr" " no"
+.BI "-[no]bhamsr" "no "
extract Buckingham SR energies
-.BI "-[no]bhamlr" " no"
+.BI "-[no]bhamlr" "no "
extract Buckingham LR energies
-.BI "-[no]free" " yes"
+.BI "-[no]free" "yes "
calculate free energy
-.BI "-temp" " real" " 300"
+.BI "-temp" " real" " 300 "
reference temperature for free energy calculation
-.TH g_energy 1 "Mon 29 Aug 2005"
+.TH g_energy 1 "Mon 22 Sep 2008"
.SH NAME
g_energy
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_energy\fP
.BI "-f" " ener.edr "
.BI "-[no]sum" ""
.BI "-[no]dp" ""
.BI "-[no]mutot" ""
+.BI "-[no]uni" ""
.BI "-skip" " int "
.BI "-[no]aver" ""
.BI "-nmol" " int "
Average and RMSD 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. Total drift is drift
-multiplied by total time.
+multiplied by total time. The term fluctuation gives the RMSD around
+the LSQ fit.
When the
.SH FILES
.BI "-f" " ener.edr"
.B Input
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-f2" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-s" " topol.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " energy.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]fee" " no"
+.BI "-[no]fee" "no "
Do a free energy estimate
-.BI "-fetemp" " real" " 300"
+.BI "-fetemp" " real" " 300 "
Reference temperature for free energy calculation
-.BI "-zero" " real" " 0"
+.BI "-zero" " real" " 0 "
Subtract a zero-point energy
-.BI "-[no]sum" " no"
+.BI "-[no]sum" "no "
Sum the energy terms selected rather than display them all
-.BI "-[no]dp" " no"
+.BI "-[no]dp" "no "
Print energies in high precision
-.BI "-[no]mutot" " no"
+.BI "-[no]mutot" "no "
Compute the total dipole moment from the components
+.BI "-[no]uni" "yes "
+ Skip non-uniformly spaced frames
+
.BI "-skip" " int" " 0"
Skip number of frames between data points
-.BI "-[no]aver" " no"
+.BI "-[no]aver" "no "
Print also the X1,t and sigma1,t, only if only 1 energy is requested
.BI "-nmol" " int" " 1"
.BI "-ndf" " int" " 3"
Number of degrees of freedom per molecule. Necessary for calculating the heat capacity
-.BI "-[no]fluc" " no"
+.BI "-[no]fluc" "no "
Calculate autocorrelation of energy fluctuations rather than energy itself
-.BI "-[no]orinst" " no"
+.BI "-[no]orinst" "no "
Analyse instantaneous orientation data
-.BI "-[no]ovec" " no"
+.BI "-[no]ovec" "no "
Also plot the eigenvectors with -oten
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_filter 1 "Mon 29 Aug 2005"
+.TH g_filter 1 "Mon 22 Sep 2008"
.SH NAME
g_filter
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_filter\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-ol" " lowpass.xtc"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-oh" " highpass.xtc"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
.BI "-nf" " int" " 10"
Sets the filter length as well as the output interval for low-pass filtering
-.BI "-[no]all" " no"
+.BI "-[no]all" "no "
Write all low-pass filtered frames
-.BI "-[no]nojump" " yes"
+.BI "-[no]nojump" "yes "
Remove jumps of atoms across the box
-.BI "-[no]fit" " no"
+.BI "-[no]fit" "no "
Fit all frames to a reference structure
-.TH g_gyrate 1 "Mon 29 Aug 2005"
+.TH g_gyrate 1 "Mon 22 Sep 2008"
.SH NAME
g_gyrate
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_gyrate\fP
.BI "-f" " traj.xtc "
.BI "-[no]q" ""
.BI "-[no]p" ""
.BI "-[no]moi" ""
+.BI "-nz" " int "
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.BI "-P" " enum "
g_gyrate computes the radius of gyration of a group of atoms
and the radii of gyration about the x, y and z axes,
as a function of time. The atoms are explicitly mass weighted.
+
+
With the
.B -nmol
option the radius of gyration will be calculated
for multiple molecules by splitting the analysis group in equally
sized parts.
+
+
+With the option
+.B -nz
+2D radii of gyration in the x-y plane
+of slices along the z-axis are calculated.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-nmol" " int" " 1"
The number of molecules to analyze
-.BI "-[no]q" " no"
+.BI "-[no]q" "no "
Use absolute value of the charge of an atom as weighting factor instead of mass
-.BI "-[no]p" " no"
+.BI "-[no]p" "no "
Calculate the radii of gyration about the principal axes.
-.BI "-[no]moi" " no"
- Calculate the moments of inertia (defined by the principal axes).
+.BI "-[no]moi" "no "
+ Calculate the moments of inertia (defined by the principal axes).
+
+.BI "-nz" " int" " 0"
+ Calculate the 2D radii of gyration of slices along the z-axis
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_h2order 1 "Mon 29 Aug 2005"
+.TH g_h2order 1 "Mon 22 Sep 2008"
.SH NAME
g_h2order
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_h2order\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " order.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-d" " string" " Z"
.BI "-sl" " int" " 0"
Calculate order parameter as function of boxlength, dividing the box in nr slices.
+.SH KNOWN PROBLEMS
\- 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.
-.TH g_hbond 1 "Mon 29 Aug 2005"
+.TH g_hbond 1 "Mon 22 Sep 2008"
.SH NAME
g_hbond
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_hbond\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
-.BI "-g" " hbond.log "
-.BI "-sel" " select.ndx "
.BI "-num" " hbnum.xvg "
+.BI "-g" " hbond.log "
.BI "-ac" " hbac.xvg "
.BI "-dist" " hbdist.xvg "
.BI "-ang" " hbang.xvg "
.BI "-don" " donor.xvg "
.BI "-dan" " danum.xvg "
.BI "-life" " hblife.xvg "
+.BI "-nhbdist" " nhbdist.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-a" " real "
.BI "-r" " real "
.BI "-[no]da" ""
+.BI "-r2" " real "
.BI "-abin" " real "
.BI "-rbin" " real "
.BI "-[no]nitacc" ""
.BI "-shell" " real "
.BI "-fitstart" " real "
.BI "-temp" " real "
+.BI "-smooth" " real "
.BI "-dump" " int "
.BI "-max_hb" " real "
.BI "-[no]merge" ""
.BI "-endfit" " real "
.SH DESCRIPTION
g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
-determined based on cutoffs for the angle Donor - Hydrogen - Acceptor
+determined based on cutoffs for the angle Acceptor - Donor - Hydrogen
(zero is extended) and the distance Hydrogen - Acceptor.
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
bonds between atoms within the shell distance from the one atom are
considered.
-It is also possible to analyse specific hydrogen bonds with
-
-.B -sel
-. This index file must contain a group of atom triplets
-Donor Hydrogen Acceptor, in the following way:
-
-
.B
[ selected ]
.
+.B -nhbdist
+: compute the number of HBonds per hydrogen in order to
+compare results to Raman Spectroscopy.
+
+
Note: options
.B -ac
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
-.BI "-g" " hbond.log"
-.B Output, Opt.
- Log file
-
-.BI "-sel" " select.ndx"
-.B Input, Opt.
- Index file
-
.BI "-num" " hbnum.xvg"
.B Output
xvgr/xmgr file
+.BI "-g" " hbond.log"
+.B Output, Opt.
+ Log file
+
.BI "-ac" " hbac.xvg"
.B Output, Opt.
xvgr/xmgr file
.B Output, Opt.
xvgr/xmgr file
+.BI "-nhbdist" " nhbdist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]ins" " no"
+.BI "-[no]ins" "no "
Analyze solvent insertion
-.BI "-a" " real" " 30"
- Cutoff angle (degrees, Donor - Hydrogen - Acceptor)
+.BI "-a" " real" " 30 "
+ Cutoff angle (degrees, Acceptor - Donor - Hydrogen)
-.BI "-r" " real" " 0.35"
+.BI "-r" " real" " 0.35 "
Cutoff radius (nm, X - Acceptor, see next option)
-.BI "-[no]da" " yes"
+.BI "-[no]da" "yes "
Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)
-.BI "-abin" " real" " 1"
+.BI "-r2" " real" " 0 "
+ Second cutoff radius. Mainly useful with -contact and -ac
+
+.BI "-abin" " real" " 1 "
Binwidth angle distribution (degrees)
-.BI "-rbin" " real" " 0.005"
+.BI "-rbin" " real" " 0.005 "
Binwidth distance distribution (nm)
-.BI "-[no]nitacc" " yes"
+.BI "-[no]nitacc" "yes "
Regard nitrogen atoms as acceptors
-.BI "-[no]contact" " no"
+.BI "-[no]contact" "no "
Do not look for hydrogen bonds, but merely for contacts within the cut-off distance
-.BI "-shell" " real" " -1"
+.BI "-shell" " real" " -1 "
when 0, only calculate hydrogen bonds within nm shell around one particle
-.BI "-fitstart" " real" " 1"
- Time from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation
+.BI "-fitstart" " real" " 1 "
+ 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
.BI "-temp" " real" " 298.15"
Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming
+.BI "-smooth" " real" " -1 "
+ If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)
+
.BI "-dump" " int" " 0"
Dump the first N hydrogen bond ACFs in a single xvg file for debugging
-.BI "-max_hb" " real" " 0"
+.BI "-max_hb" " real" " 0 "
Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly
-.BI "-[no]merge" " yes"
+.BI "-[no]merge" "yes "
H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF.
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
+.SH KNOWN PROBLEMS
+\- The option
+.B -sel
+that used to work on selected hbonds is out of order, and therefore not available for the time being.
+
-.TH g_helix 1 "Mon 29 Aug 2005"
+.TH g_helix 1 "Mon 22 Sep 2008"
.SH NAME
g_helix
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_helix\fP
.BI "-s" " topol.tpr "
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-to" " gtraj.g87"
.B Output, Opt.
.BI "-cz" " zconf.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-co" " waver.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
.BI "-r0" " int" " 1"
The first residue number in the sequence
-.BI "-[no]q" " no"
+.BI "-[no]q" "no "
Check at every step which part of the sequence is helical
-.BI "-[no]F" " yes"
+.BI "-[no]F" "yes "
Toggle fit to a perfect helix
-.BI "-[no]db" " no"
+.BI "-[no]db" "no "
Print debug info
.BI "-prop" " enum" " RAD"
.B CD222
-.BI "-[no]ev" " no"
+.BI "-[no]ev" "no "
Write a new 'trajectory' file for ED
.BI "-ahxstart" " int" " 0"
-.TH g_lie 1 "Mon 29 Aug 2005"
+.TH g_lie 1 "Mon 22 Sep 2008"
.SH NAME
g_lie
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_lie\fP
.BI "-f" " ener.edr "
.SH FILES
.BI "-f" " ener.edr"
.B Input
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-o" " lie.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-Elj" " real" " 0"
+.BI "-Elj" " real" " 0 "
Lennard-Jones interaction between ligand and solvent
-.BI "-Eqq" " real" " 0"
+.BI "-Eqq" " real" " 0 "
Coulomb interaction between ligand and solvent
-.BI "-Clj" " real" " 0.181"
+.BI "-Clj" " real" " 0.181 "
Factor in the LIE equation for Lennard-Jones component of energy
-.BI "-Cqq" " real" " 0.5"
+.BI "-Cqq" " real" " 0.5 "
Factor in the LIE equation for Coulomb component of energy
.BI "-ligand" " string" " none"
-.TH g_mdmat 1 "Mon 29 Aug 2005"
+.TH g_mdmat 1 "Mon 22 Sep 2008"
.SH NAME
g_mdmat
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_mdmat\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-t" " real" " 1.5"
+.BI "-t" " real" " 1.5 "
trunc distance
.BI "-nlevels" " int" " 40"
-.TH g_mindist 1 "Mon 29 Aug 2005"
+.TH g_mindist 1 "Mon 22 Sep 2008"
.SH NAME
g_mindist
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_mindist\fP
.BI "-f" " traj.xtc "
.BI "-[no]pi" ""
.BI "-[no]split" ""
.BI "-ng" " int "
+.BI "-[no]pbc" ""
.SH DESCRIPTION
g_mindist computes the distance between one group and a number of
other groups. Both the minimum distance
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-ox" " mindist.xtc"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-or" " mindistres.xvg"
.B Output, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]matrix" " no"
+.BI "-[no]matrix" "no "
Calculate half a matrix of group-group distances
-.BI "-[no]max" " no"
+.BI "-[no]max" "no "
Calculate *maximum* distance instead of minimum
-.BI "-d" " real" " 0.6"
+.BI "-d" " real" " 0.6 "
Distance for contacts
-.BI "-[no]pi" " no"
+.BI "-[no]pi" "no "
Calculate minimum distance with periodic images
-.BI "-[no]split" " no"
+.BI "-[no]split" "no "
Split graph where time is zero
.BI "-ng" " int" " 1"
Number of secondary groups to compute distance to a central group
+.BI "-[no]pbc" "yes "
+ Take periodic boundary conditions into account
+
-.TH g_morph 1 "Mon 29 Aug 2005"
+.TH g_morph 1 "Mon 22 Sep 2008"
.SH NAME
g_morph
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_morph\fP
.BI "-f1" " conf1.gro "
.SH FILES
.BI "-f1" " conf1.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-f2" " conf2.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " interm.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-or" " rms-interm.xvg"
.B Output, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-ninterm" " int" " 11"
Number of intermediates
-.BI "-first" " real" " 0"
+.BI "-first" " real" " 0 "
Corresponds to first generated structure (0 is input x0, see above)
-.BI "-last" " real" " 1"
+.BI "-last" " real" " 1 "
Corresponds to last generated structure (1 is input x1, see above)
-.BI "-[no]fit" " yes"
+.BI "-[no]fit" "yes "
Do a least squares fit of the second to the first structure before interpolating
-.TH g_msd 1 "Mon 29 Aug 2005"
+.TH g_msd 1 "Mon 22 Sep 2008"
.SH NAME
g_msd
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_msd\fP
.BI "-f" " traj.xtc "
.BI "-n" " index.ndx "
.BI "-o" " msd.xvg "
.BI "-mol" " diff_mol.xvg "
+.BI "-pdb" " diff_mol.pdb "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-[no]xvgr" ""
.BI "-type" " enum "
.BI "-lateral" " enum "
+.BI "-[no]ten" ""
.BI "-ngroup" " int "
.BI "-[no]mw" ""
+.BI "-[no]rmcomm" ""
+.BI "-tpdb" " time "
.BI "-trestart" " time "
.BI "-beginfit" " time "
.BI "-endfit" " time "
of the fit interval.
+There are three, mutually exclusive, options to determine different
+types of mean square displacement:
+.B -type
+,
+.B -lateral
+
+and
+.B -ten
+. Option
+.B -ten
+writes the full MSD tensor for
+each group, the order in the output is: trace xx yy zz yx zx zy.
+
+
Option
.B -mol
plots the MSD for molecules, this implies
+With option
+.B -rmcomm
+center of mass motion can be removed.
+For trajectories produced with GROMACS this is usually not necessary
+as mdrun 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.
+
+
.B -mw
, i.e. for each inidividual molecule an diffusion constant
-is computed. When using an index file, it should contain molecule
-numbers instead of atom numbers.
+is computed for its center of mass. The chosen index group will
+be split into molecules.
+The diffusion coefficient is determined by linear regression of the MSD,
+where, unlike for the normal output of D, the times are weighted
+according to the number of restart point, i.e. short times have
+a higher weight. Also when
+.B -beginfit
+=-1,fitting starts at 0
+and when
+.B -endfit
+=-1, fitting goes to the end.
Using this option one also gets an accurate error estimate
-based on the statistics between individual molecules. Since one usually
-is interested in self-diffusion at infinite dilution this is probably
-the most useful number.
+based on the statistics between individual molecules.
+Note that this diffusion coefficient and error estimate are only
+accurate when the MSD is completely linear between
+
+.B -beginfit
+and
+.B -endfit
+.
+Option
+.B -pdb
+writes a pdb file with the coordinates of the frame
+at time
+.B -tpdb
+with in the B-factor field the square root of
+the diffusion coefficient of the molecule.
+This option implies option
+.B -mol
+.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
+.BI "-pdb" " diff_mol.pdb"
+.B Output, Opt.
+ Protein data bank file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-type" " enum" " no"
.B z
+.BI "-[no]ten" "no "
+ Calculate the full tensor
+
.BI "-ngroup" " int" " 1"
Number of groups to calculate MSD for
-.BI "-[no]mw" " yes"
+.BI "-[no]mw" "yes "
Mass weighted MSD
-.BI "-trestart" " time" " 10"
+.BI "-[no]rmcomm" "no "
+ Remove center of mass motion
+
+.BI "-tpdb" " time" " 0 "
+ The frame to use for option -pdb (ps)
+
+.BI "-trestart" " time" " 10 "
Time between restarting points in trajectory (ps)
-.BI "-beginfit" " time" " -1"
+.BI "-beginfit" " time" " -1 "
Start time for fitting the MSD (ps), -1 is 10%
-.BI "-endfit" " time" " -1"
+.BI "-endfit" " time" " -1 "
End time for fitting the MSD (ps), -1 is 90%
-.TH g_nmeig 1 "Mon 29 Aug 2005"
+.TH g_nmeig 1 "Mon 22 Sep 2008"
.SH NAME
g_nmeig
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_nmeig\fP
.BI "-f" " hessian.mtx "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-of" " eigenfreq.xvg"
.B Output
.BI "-v" " eigenvec.trr"
.B Output
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]m" " yes"
+.BI "-[no]m" "yes "
Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis
.BI "-first" " int" " 1"
-.TH g_nmens 1 "Mon 29 Aug 2005"
+.TH g_nmens 1 "Mon 22 Sep 2008"
.SH NAME
g_nmens
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_nmens\fP
.BI "-v" " eigenvec.trr "
.SH FILES
.BI "-v" " eigenvec.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-e" " eigenval.xvg"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " ensemble.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-temp" " real" " 300"
+.BI "-temp" " real" " 300 "
Temperature in Kelvin
.BI "-seed" " int" " -1"
-.TH g_nmtraj 1 "Tue 6 Sep 2005"
+.TH g_nmtraj 1 "Mon 22 Sep 2008"
.SH NAME
g_nmtraj
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_nmtraj\fP
.BI "-s" " topol.tpr "
.BI "-o" " nmtraj.xtc "
.BI "-[no]h" ""
.BI "-nice" " int "
-.BI "-eignr" " int "
+.BI "-eignr" " string "
+.BI "-phases" " string "
.BI "-temp" " real "
.BI "-amplitude" " real "
.BI "-nframes" " int "
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-v" " eigenvec.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-o" " nmtraj.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-eignr" " int" " 7"
- Eigenvector to use (first is 1)
+.BI "-eignr" " string" " 7"
+ String of eigenvectors to use (first is 1)
-.BI "-temp" " real" " 300"
+.BI "-phases" " string" " 0.0"
+ String of phases (default is 0.0)
+
+.BI "-temp" " real" " 300 "
Temperature in Kelvin
-.BI "-amplitude" " real" " 0.25"
+.BI "-amplitude" " real" " 0.25 "
Amplitude for modes with eigenvalue=0
.BI "-nframes" " int" " 30"
-.TH g_order 1 "Mon 29 Aug 2005"
+.TH g_order 1 "Mon 22 Sep 2008"
.SH NAME
g_order
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_order\fP
.BI "-f" " traj.xtc "
.BI "-o" " order.xvg "
.BI "-od" " deuter.xvg "
.BI "-os" " sliced.xvg "
+.BI "-Sg" " sg-ang.xvg "
+.BI "-Sk" " sk-dist.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
order parameter per slice is calculated as well. If -szonly is not
selected, all diagonal elements and the deuterium order parameter is
given.
+
+The tetrahedrality order parameters can be determined
+around an 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.
+
+
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " order.xvg"
.B Output
.B Output
xvgr/xmgr file
+.BI "-Sg" " sg-ang.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-Sk" " sk-dist.xvg"
+.B Output
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-d" " enum" " z"
.BI "-sl" " int" " 1"
Calculate order parameter as function of boxlength, dividing the box in nr slices.
-.BI "-[no]szonly" " no"
+.BI "-[no]szonly" "no "
Only give Sz element of order tensor. (axis can be specified with -d)
-.BI "-[no]unsat" " no"
+.BI "-[no]unsat" "no "
Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.
-.TH g_potential 1 "Mon 29 Aug 2005"
+.TH g_potential 1 "Mon 22 Sep 2008"
.SH NAME
g_potential
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_potential\fP
.BI "-f" " traj.xtc "
.BI "-tz" " real "
.BI "-[no]spherical" ""
.BI "-ng" " int "
+.BI "-[no]correct" ""
.SH DESCRIPTION
Compute the electrostatical potential across the box. The potential iscalculated by first summing the charges per slice and then integratingtwice of this charge distribution. Periodic boundaries are not taken into account. Reference of potential is taken to be the left side ofthe box. It's also possible to calculate the potential in sphericalcoordinates as function of r by calculating a charge distribution inspherical slices and twice integrating them. epsilon_r is taken as 1,2 is more appropriate in many cases
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " potential.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-d" " string" " Z"
.BI "-ce" " int" " 0"
Discard last nr slices of box for integration
-.BI "-tz" " real" " 0"
+.BI "-tz" " real" " 0 "
Translate all coordinates distance in the direction of the box
-.BI "-[no]spherical" " no"
+.BI "-[no]spherical" "no "
Calculate spherical thingie
.BI "-ng" " int" " 1"
Number of groups to consider
+.BI "-[no]correct" "no "
+ Assume net zero charge of groups to improve accuracy
+
+.SH KNOWN PROBLEMS
\- Discarding slices for integration should not be necessary.
-.TH g_rama 1 "Mon 29 Aug 2005"
+.TH g_rama 1 "Mon 22 Sep 2008"
.SH NAME
g_rama
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rama\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " rama.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.TH g_rdf 1 "Mon 29 Aug 2005"
+.TH g_rdf 1 "Mon 22 Sep 2008"
.SH NAME
g_rdf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rdf\fP
.BI "-f" " traj.xtc "
.BI "-[no]xvgr" ""
.BI "-bin" " real "
.BI "-[no]com" ""
+.BI "-rdf" " enum "
.BI "-[no]pbc" ""
+.BI "-[no]norm" ""
.BI "-[no]xy" ""
.BI "-cut" " real "
.BI "-ng" " int "
.
+The option
+.B -rdf
+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
+the atoms in the index groups are taken into account.
+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
+by providing a run input file with different masses.
+Option
+.B -com
+also works in conjunction with
+.B -rdf
+.
+
If a run input file is supplied (
.B -s
-), exclusions defined
+) and
+.B -rdf
+is set
+to
+.B atom
+, exclusions defined
in that file are taken into account when calculating the rdf.
The option
.B -cut
Option
.B -cn
-produces the cumulative number rdf.
+produces the cumulative number rdf,
+i.e. the average number of particles within a distance r.
+
To bridge the gap between theory and experiment structure factors can
be computed (option
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-bin" " real" " 0.002"
+.BI "-bin" " real" " 0.002 "
Binwidth (nm)
-.BI "-[no]com" " no"
+.BI "-[no]com" "no "
RDF with respect to the center of mass of first group
-.BI "-[no]pbc" " yes"
- Use periodic boundary conditions for computing distances
+.BI "-rdf" " enum" " atom"
+ RDF type:
+.B atom
+,
+.B mol_com
+,
+.B mol_cog
+,
+.B res_com
+or
+.B res_cog
+
+
+.BI "-[no]pbc" "yes "
+ Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the larges box edge.
+
+.BI "-[no]norm" "yes "
+ Normalize for volume and density
-.BI "-[no]xy" " no"
+.BI "-[no]xy" "no "
Use only the x and y components of the distance
-.BI "-cut" " real" " 0"
+.BI "-cut" " real" " 0 "
Shortest distance (nm) to be considered
.BI "-ng" " int" " 1"
Number of secondary groups to compute RDFs around a central group
-.BI "-fade" " real" " 0"
+.BI "-fade" " real" " 0 "
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.
.BI "-nlevel" " int" " 20"
Number of different colors in the diffraction image
-.BI "-startq" " real" " 0"
+.BI "-startq" " real" " 0 "
Starting q (1/nm)
-.BI "-endq" " real" " 60"
+.BI "-endq" " real" " 60 "
Ending q (1/nm)
-.BI "-energy" " real" " 12"
+.BI "-energy" " real" " 12 "
Energy of the incoming X-ray (keV)
-.TH g_rms 1 "Mon 29 Aug 2005"
+.TH g_rms 1 "Mon 22 Sep 2008"
.SH NAME
g_rms
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rms\fP
.BI "-s" " topol.tpr "
.BI "-min" " real "
.BI "-bmax" " real "
.BI "-bmin" " real "
+.BI "-[no]mw" ""
.BI "-nlevels" " int "
.BI "-ng" " int "
.SH DESCRIPTION
translation), translation only, or no fitting at all.
+Option
+.B -mw
+controls whether mass weighting is done or not.
+If you select the option (default) and
+supply a valid tpr file masses will be taken from there,
+otherwise the masses will be deduced from the atommass.dat 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)
+is assigned to unknown atoms. You can check whether this happend by
+turning on the
+.B -debug
+flag and inspecting the log file.
+
+
With
.B -f2
, the 'other structures' are taken from a second
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-f2" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input, Opt.
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-what" " enum" " rmsd"
.B rhosc
-.BI "-[no]pbc" " yes"
+.BI "-[no]pbc" "yes "
PBC check
.BI "-fit" " enum" " rot+trans"
.BI "-prev" " int" " 0"
Compare with previous frame
-.BI "-[no]split" " no"
+.BI "-[no]split" "no "
Split graph where time is zero
.BI "-skip" " int" " 1"
.BI "-skip2" " int" " 1"
Only write every nr-th frame to matrix
-.BI "-max" " real" " -1"
+.BI "-max" " real" " -1 "
Maximum level in comparison matrix
-.BI "-min" " real" " -1"
+.BI "-min" " real" " -1 "
Minimum level in comparison matrix
-.BI "-bmax" " real" " -1"
+.BI "-bmax" " real" " -1 "
Maximum level in bond angle matrix
-.BI "-bmin" " real" " -1"
+.BI "-bmin" " real" " -1 "
Minimum level in bond angle matrix
+.BI "-[no]mw" "yes "
+ Use mass weighting for superposition
+
.BI "-nlevels" " int" " 80"
Number of levels in the matrices
-.TH g_rmsdist 1 "Mon 29 Aug 2005"
+.TH g_rmsdist 1 "Mon 22 Sep 2008"
.SH NAME
g_rmsdist
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rmsdist\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Generic data file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-nlevels" " int" " 40"
Discretize rms in levels
-.BI "-max" " real" " -1"
+.BI "-max" " real" " -1 "
Maximum level in matrices
-.BI "-[no]sumh" " yes"
+.BI "-[no]sumh" "yes "
average distance over equivalent hydrogens
-.TH g_rmsf 1 "Mon 29 Aug 2005"
+.TH g_rmsf 1 "Mon 22 Sep 2008"
.SH NAME
g_rmsf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "-f" " traj.xtc "
.BI "-[no]xvgr" ""
.BI "-[no]res" ""
.BI "-[no]aniso" ""
+.BI "-[no]fit" ""
.SH DESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
deviation) of atomic positions
-after first fitting to a reference frame.
+after (optionally) fitting to a reference frame.
With option
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Log file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]res" " no"
+.BI "-[no]res" "no "
Calculate averages for each residue
-.BI "-[no]aniso" " no"
+.BI "-[no]aniso" "no "
Compute anisotropic termperature factors
+.BI "-[no]fit" "yes "
+ Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.
+
-.TH g_rotacf 1 "Mon 29 Aug 2005"
+.TH g_rotacf 1 "Mon 22 Sep 2008"
.SH NAME
g_rotacf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rotacf\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]d" " no"
+.BI "-[no]d" "no "
Use index doublets (vectors) for correlation function instead of triplets (planes)
-.BI "-[no]aver" " yes"
+.BI "-[no]aver" "yes "
Average over molecules
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_saltbr 1 "Mon 29 Aug 2005"
+.TH g_saltbr 1 "Mon 22 Sep 2008"
.SH NAME
g_saltbr
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_saltbr\fP
.BI "-f" " traj.xtc "
.BI "-t" " real "
.BI "-[no]sep" ""
.SH DESCRIPTION
-g_saltbr plots the difference between all combination of charged groups
+g_saltbr 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.
-Output will be in a number of fixed filenames, min-min.xvg,min-plus.xvg
+Output will be in a number of fixed filenames, min-min.xvg, plus-min.xvg
and plus-plus.xvg, or files for every individual ion-pair if selected
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-t" " real" " 1000"
+.BI "-t" " real" " 1000 "
trunc distance
-.BI "-[no]sep" " no"
+.BI "-[no]sep" "no "
Use separate files for each interaction (may be MANY)
-.TH g_sas 1 "Mon 29 Aug 2005"
+.TH g_sas 1 "Mon 22 Sep 2008"
.SH NAME
g_sas
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_sas\fP
.BI "-f" " traj.xtc "
.BI "-o" " area.xvg "
.BI "-or" " resarea.xvg "
.BI "-oa" " atomarea.xvg "
+.BI "-tv" " volume.xvg "
.BI "-q" " connelly.pdb "
.BI "-n" " index.ndx "
.BI "-i" " surfat.itp "
.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
-.BI "-solsize" " real "
+.BI "-probe" " real "
.BI "-ndots" " int "
.BI "-qmax" " real "
.BI "-[no]f_index" ""
.BI "-minarea" " real "
-.BI "-[no]pbc" ""
.BI "-[no]prot" ""
.BI "-dgs" " real "
.SH DESCRIPTION
this can be turned off using the
.B -pbc
option.
+
+
+With the
+.B -tv
+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.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " area.xvg"
.B Output
.B Output, Opt.
xvgr/xmgr file
+.BI "-tv" " volume.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-q" " connelly.pdb"
.B Output, Opt.
Protein data bank file
Include file for topology
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-solsize" " real" " 0.14"
+.BI "-probe" " real" " 0.14 "
Radius of the solvent probe (nm)
.BI "-ndots" " int" " 24"
Number of dots per sphere, more dots means more accuracy
-.BI "-qmax" " real" " 0.2"
+.BI "-qmax" " real" " 0.2 "
The maximum charge (e, absolute value) of a hydrophobic atom
-.BI "-[no]f_index" " no"
+.BI "-[no]f_index" "no "
Determine from a group in the index file what are the hydrophobic atoms rather than from the charge
-.BI "-minarea" " real" " 0.5"
+.BI "-minarea" " real" " 0.5 "
The minimum area (nm2) to count an atom as a surface atom when writing a position restraint file (see help)
-.BI "-[no]pbc" " yes"
- Take periodicity into account
-
-.BI "-[no]prot" " yes"
+.BI "-[no]prot" "yes "
Output the protein to the connelly pdb file too
-.BI "-dgs" " real" " 0"
+.BI "-dgs" " real" " 0 "
default value for solvation free energy per area (kJ/mol/nm2)
-.TH g_sgangle 1 "Mon 29 Aug 2005"
+.TH g_sgangle 1 "Mon 22 Sep 2008"
.SH NAME
g_sgangle
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_sgangle\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
-.BI "-[no]pbc" ""
.BI "-[no]one" ""
.BI "-[no]z" ""
.SH DESCRIPTION
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-oa" " sg_angle.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]pbc" " no"
- Use periodic boundary conditions
-
-.BI "-[no]one" " no"
+.BI "-[no]one" "no "
Only one group compute angle between vector at time zero and time t
-.BI "-[no]z" " no"
+.BI "-[no]z" "no "
Use the Z-axis as reference
-.TH g_sham 1 "Mon 29 Aug 2005"
+.TH g_sham 1 "Mon 22 Sep 2008"
.SH NAME
g_sham
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_sham\fP
.BI "-f" " graph.xvg "
.BI "-dist" " ener.xvg "
.BI "-histo" " edist.xvg "
.BI "-bin" " bindex.ndx "
+.BI "-lp" " prob.xpm "
.BI "-ls" " gibbs.xpm "
.BI "-lsh" " enthalpy.xpm "
.BI "-lss" " entropy.xpm "
.BI "-ngrid" " vector "
.BI "-xmin" " vector "
.BI "-xmax" " vector "
+.BI "-pmax" " real "
.BI "-gmax" " real "
+.BI "-emin" " real "
+.BI "-emax" " real "
.BI "-nlevels" " int "
.BI "-mname" " string "
.SH DESCRIPTION
-g_sham reads a number of xvg files and analyzes data sets.
+g_sham makes multi-dimensional free-energy, enthalpy and entropy plots.
+g_sham reads one or more xvg files and analyzes data sets.
+g_sham basic purpose is plotting Gibbs free energy landscapes
+(option
+.B -ls
+)
+by Bolzmann inverting multi-dimensional histograms (option
+.B -lp
+)
+but it can also
+make enthalpy (option
+.B -lsh
+) and entropy (option
+.B -lss
+)
+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
.B -time
Option
.B -ge
can be used to supply a file with free energies
-when the ensemble is not a Boltzmann ensemble, but has been biased
-by this free energy.
+when the ensemble is not a Boltzmann ensemble, but needs to be biased
+by this free energy. One free energy value is required for each
+(multi-dimensional) data point in the
+.B -f
+input.
+
+
+
+Option
+.B -ene
+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
+weighting scheme is applied. In addition the vales
+are used for making enthalpy and entropy plots.
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 free-energy for this volume effect.
+the histogram and free-energy for this volume effect.
The probability is normalized by r and r2 for a dimension 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
is the natural quantity to use, as it will produce bins of the same
volume.
.B Output, Opt.
Index file
+.BI "-lp" " prob.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
.BI "-ls" " gibbs.xpm"
.B Output, Opt.
X PixMap compatible matrix file
Log file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]time" " yes"
+.BI "-[no]time" "yes "
Expect a time in the input
-.BI "-b" " real" " -1"
+.BI "-b" " real" " -1 "
First time to read from set
-.BI "-e" " real" " -1"
+.BI "-e" " real" " -1 "
Last time to read from set
-.BI "-ttol" " real" " 0"
+.BI "-ttol" " real" " 0 "
Tolerance on time in appropriate units (usually ps)
.BI "-n" " int" " 1"
Read sets seperated by &
-.BI "-[no]d" " no"
+.BI "-[no]d" "no "
Use the derivative
-.BI "-bw" " real" " 0.1"
+.BI "-bw" " real" " 0.1 "
Binwidth for the distribution
-.BI "-[no]sham" " yes"
+.BI "-[no]sham" "yes "
Turn off energy weighting even if energies are given
.BI "-tsham" " real" " 298.15"
Temperature for single histogram analysis
-.BI "-pmin" " real" " 0"
+.BI "-pmin" " real" " 0 "
Minimum probability. Anything lower than this will be set to zero
.BI "-dim" " vector" " 1 1 1"
.BI "-xmax" " vector" " 1 1 1"
Maximum for the axes in energy landscape (see above for 3 dimensions)
-.BI "-gmax" " real" " 0"
- Maximum level in output, 0 is calculate
+.BI "-pmax" " real" " 0 "
+ Maximum probability in output, default is calculate
+
+.BI "-gmax" " real" " 0 "
+ Maximum free energy in output, default is calculate
+
+.BI "-emin" " real" " 0 "
+ Minimum enthalpy in output, default is calculate
+
+.BI "-emax" " real" " 0 "
+ Maximum enthalpy in output, default is calculate
.BI "-nlevels" " int" " 25"
- Number of levels for energy landscape from single histogram analysis
+ Number of levels for energy landscape
.BI "-mname" " string" " "
Legend label for the custom landscape
-.TH g_sorient 1 "Mon 29 Aug 2005"
+.TH g_sorient 1 "Mon 22 Sep 2008"
.SH NAME
g_sorient
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_sorient\fP
.BI "-f" " traj.xtc "
.BI "-no" " snor.xvg "
.BI "-ro" " sord.xvg "
.BI "-co" " scum.xvg "
+.BI "-rc" " scount.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
.BI "-[no]com" ""
+.BI "-[no]v23" ""
.BI "-rmin" " real "
.BI "-rmax" " real "
-.BI "-bin" " real "
+.BI "-cbin" " real "
+.BI "-rbin" " real "
.BI "-[no]pbc" ""
.SH DESCRIPTION
g_sorient analyzes solvent orientation around solutes.
molecule to the midpoint between atoms 2 and 3.
theta2: the angle with the normal of the solvent plane, defined by the
-same three atoms.
+same three atoms, or when the option
+.B -v23
+is set
+the angle with the vector between atoms 2 and 3.
The reference can be a set of atoms or
the center of mass of a set of atoms. The group of solvent atoms should
.B -no
-: distribution of 3cos2(theta2)-1 for rmin=r=rmax.
+: distribution of cos(theta2) for rmin=r=rmax.
of cos(theta1) and 3cos2(theta2)-1 as a function of r.
+
+.B -rc
+: the distribution of the solvent molecules as a function of r
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output
xvgr/xmgr file
+.BI "-rc" " scount.xvg"
+.B Output
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]com" " no"
+.BI "-[no]com" "no "
Use the center of mass as the reference postion
-.BI "-rmin" " real" " 0"
- Minimum distance
+.BI "-[no]v23" "no "
+ Use the vector between atoms 2 and 3
+
+.BI "-rmin" " real" " 0 "
+ Minimum distance (nm)
+
+.BI "-rmax" " real" " 0.5 "
+ Maximum distance (nm)
-.BI "-rmax" " real" " 0.5"
- Maximum distance
+.BI "-cbin" " real" " 0.02 "
+ Binwidth for the cosine
-.BI "-bin" " real" " 0.02"
- Binwidth
+.BI "-rbin" " real" " 0.02 "
+ Binwidth for r (nm)
-.BI "-[no]pbc" " no"
+.BI "-[no]pbc" "no "
Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.
-.TH g_tcaf 1 "Mon 29 Aug 2005"
+.TH g_tcaf 1 "Mon 22 Sep 2008"
.SH NAME
g_tcaf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_tcaf\fP
.BI "-f" " traj.trr "
.SH FILES
.BI "-f" " traj.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]mol" " no"
+.BI "-[no]mol" "no "
Calculate tcaf of molecules
-.BI "-[no]k34" " no"
+.BI "-[no]k34" "no "
Also use k=(3,0,0) and k=(4,0,0)
-.BI "-wt" " real" " 5"
+.BI "-wt" " real" " 5 "
Exponential decay time for the TCAF fit weights
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_traj 1 "Mon 29 Aug 2005"
+.TH g_traj 1 "Mon 22 Sep 2008"
.SH NAME
g_traj
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_traj\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-ox" " coord.xvg "
+.BI "-oxt" " coord.xtc "
.BI "-ov" " veloc.xvg "
.BI "-of" " force.xvg "
.BI "-ob" " box.xvg "
.BI "-vd" " veldist.xvg "
.BI "-cv" " veloc.pdb "
.BI "-cf" " force.pdb "
+.BI "-av" " all_veloc.xvg "
+.BI "-af" " all_force.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
the
.B -nojump
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 xvg file as well
+(specified with
+.B -av
+or
+.B -af
+).
Option
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
+.BI "-oxt" " coord.xtc"
+.B Output, Opt.
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
.BI "-ov" " veloc.xvg"
.B Output, Opt.
xvgr/xmgr file
.B Output, Opt.
Protein data bank file
+.BI "-av" " all_veloc.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-af" " all_force.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]com" " no"
+.BI "-[no]com" "no "
Plot data for the com of each group
-.BI "-[no]mol" " no"
+.BI "-[no]mol" "no "
Index contains molecule numbers iso atom numbers
-.BI "-[no]nojump" " no"
+.BI "-[no]nojump" "no "
Remove jumps of atoms across the box
-.BI "-[no]x" " yes"
+.BI "-[no]x" "yes "
Plot X-component
-.BI "-[no]y" " yes"
+.BI "-[no]y" "yes "
Plot Y-component
-.BI "-[no]z" " yes"
+.BI "-[no]z" "yes "
Plot Z-component
.BI "-ng" " int" " 1"
Number of groups to consider
-.BI "-[no]len" " no"
+.BI "-[no]len" "no "
Plot vector length
-.BI "-bin" " real" " 1"
+.BI "-bin" " real" " 1 "
Binwidth for velocity histogram (nm/ps)
-.BI "-scale" " real" " 0"
+.BI "-scale" " real" " 0 "
Scale factor for pdb output, 0 is autoscale
-.TH g_velacc 1 "Mon 29 Aug 2005"
+.TH g_velacc 1 "Mon 22 Sep 2008"
.SH NAME
g_velacc
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_velacc\fP
.BI "-f" " traj.trr "
.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
+.BI "-[no]m" ""
.BI "-[no]mol" ""
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.SH DESCRIPTION
g_velacc computes the velocity autocorrelation function.
When the
-.B -s
+.B -m
option is used, the momentum autocorrelation
function is calculated.
.SH FILES
.BI "-f" " traj.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]mol" " no"
- Calculate vac of molecules
+.BI "-[no]m" "no "
+ Calculate the momentum autocorrelation function
+
+.BI "-[no]mol" "no "
+ Calculate the momentum acf of molecules
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_wham 1 "Mon 29 Aug 2005"
+.TH g_wham 1 "Mon 22 Sep 2008"
.SH NAME
g_wham
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_wham\fP
.BI "-o" " profile.xvg "
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-min" " real" " 0"
+.BI "-min" " real" " 0 "
Minimum coordinate in profile
-.BI "-max" " real" " 0"
+.BI "-max" " real" " 0 "
Maximum coordinate in profile
.BI "-bins" " int" " 100"
Number of bins in profile
-.BI "-[no]prof" " yes"
+.BI "-[no]prof" "yes "
Only calculate min and max
-.BI "-temp" " real" " 298"
+.BI "-temp" " real" " 298 "
Temperature
-.BI "-[no]flip" " no"
+.BI "-[no]flip" "no "
Combine halves of profile
-.BI "-tol" " real" " 0.01"
+.BI "-tol" " real" " 0.01 "
Tolerance
-.TH genbox 1 "Mon 29 Aug 2005"
+.TH genbox 1 "Mon 22 Sep 2008"
.SH NAME
genbox
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3genbox\fP
.BI "-cp" " protein.gro "
.BI "-seed" " int "
.BI "-vdwd" " real "
.BI "-shell" " real "
+.BI "-maxsol" " int "
+.BI "-[no]vel" ""
.SH DESCRIPTION
Genbox can do one of 3 things:
) is used,
unless
.B -box
-is set, which also centers the solute.
-The program
+is set.
+If you want the solute to be centered in the box,
+the program
.B editconf
-has more sophisticated options to change
-the box and center the solute.
+has sophisticated options
+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
.SH FILES
.BI "-cp" " protein.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-cs" " spc216.gro"
.B Input, Opt., Lib.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-ci" " insert.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-p" " topol.top"
.B In/Out, Opt.
Topology file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
.BI "-seed" " int" " 1997"
random generator seed
-.BI "-vdwd" " real" " 0.105"
+.BI "-vdwd" " real" " 0.105 "
default vdwaals distance
-.BI "-shell" " real" " 0"
+.BI "-shell" " real" " 0 "
thickness of optional water layer around solute
-\- Molecules must be whole in the initial configurations.
+.BI "-maxsol" " int" " 0"
+ maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored
+
+.BI "-[no]vel" "no "
+ keep velocities from input solute and solvent
-\- At the moment -ci only works when inserting one molecule.
+.SH KNOWN PROBLEMS
+\- Molecules must be whole in the initial configurations.
-.TH genconf 1 "Mon 29 Aug 2005"
+.TH genconf 1 "Mon 22 Sep 2008"
.SH NAME
genconf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3genconf\fP
.BI "-f" " conf.gro "
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-trj" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
.BI "-seed" " int" " 0"
Random generator seed, if 0 generated from the time
-.BI "-[no]rot" " no"
+.BI "-[no]rot" "no "
Randomly rotate conformations
-.BI "-[no]shuffle" " no"
+.BI "-[no]shuffle" "no "
Random shuffling of molecules
-.BI "-[no]sort" " no"
+.BI "-[no]sort" "no "
Sort molecules on X coord
.BI "-block" " int" " 1"
.BI "-maxrot" " vector" " 90 90 90"
Maximum random rotation
-.BI "-[no]renumber" " yes"
+.BI "-[no]renumber" "yes "
Renumber residues
+.SH KNOWN PROBLEMS
\- The program should allow for random displacement off lattice points.
-.TH genion 1 "Mon 29 Aug 2005"
+.TH genion 1 "Mon 22 Sep 2008"
.SH NAME
genion
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3genion\fP
.BI "-s" " topol.tpr "
.BI "-o" " out.gro "
.BI "-g" " genion.log "
.BI "-pot" " pot.pdb "
+.BI "-p" " topol.top "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-[no]xvgr" ""
.BI "-np" " int "
.BI "-pname" " string "
-.BI "-pq" " real "
+.BI "-pq" " int "
.BI "-nn" " int "
.BI "-nname" " string "
-.BI "-nq" " real "
+.BI "-nq" " int "
.BI "-rmin" " real "
.BI "-[no]random" ""
.BI "-seed" " int "
.BI "-scale" " real "
+.BI "-conc" " real "
+.BI "-[no]neutral" ""
.SH DESCRIPTION
genion replaces solvent molecules by monoatomic ions at
the position of the first atoms with the most favorable electrostatic
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-table" " table.xvg"
.B Input, Opt.
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-g" " genion.log"
.B Output
.B Output, Opt.
Protein data bank file
+.BI "-p" " topol.top"
+.B In/Out, Opt.
+ Topology file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-np" " int" " 0"
.BI "-pname" " string" " Na"
Name of the positive ion
-.BI "-pq" " real" " 1"
+.BI "-pq" " int" " 1"
Charge of the positive ion
.BI "-nn" " int" " 0"
.BI "-nname" " string" " Cl"
Name of the negative ion
-.BI "-nq" " real" " -1"
+.BI "-nq" " int" " -1"
Charge of the negative ion
-.BI "-rmin" " real" " 0.6"
+.BI "-rmin" " real" " 0.6 "
Minimum distance between ions
-.BI "-[no]random" " no"
+.BI "-[no]random" "yes "
Use random placement of ions instead of based on potential. The rmin option should still work
.BI "-seed" " int" " 1993"
Seed for random number generator
-.BI "-scale" " real" " 0.001"
+.BI "-scale" " real" " 0.001 "
Scaling factor for the potential for -pot
+.BI "-conc" " real" " 0 "
+ 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 tpr file. Overrides the -np and nn options.
+
+.BI "-[no]neutral" "no "
+ 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.
+
+.SH KNOWN PROBLEMS
+\- Calculation of the potential is not reliable, therefore the
+.B -random
+option is now turned on by default.
+
+\- If you specify a salt concentration existing ions are not taken into account. In effect you therefore specify the amount of salt to be added.
+
-.TH gmxcheck 1 "Mon 29 Aug 2005"
+.TH gmxcheck 1 "Mon 22 Sep 2008"
.SH NAME
gmxcheck
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3gmxcheck\fP
.BI "-f" " traj.xtc "
.BI "-e" " ener.edr "
.BI "-e2" " ener2.edr "
.BI "-n" " index.ndx "
+.BI "-m" " doc.tex "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-vdwfac" " real "
.BI "-bonlo" " real "
.BI "-bonhi" " real "
.BI "-tol" " real "
+.BI "-[no]ab" ""
.BI "-lastener" " string "
.SH DESCRIPTION
gmxcheck reads a trajectory (
or
.B .xtc
-) or an energy file (
+), an energy file (
.B .ene
or
.B .edr
)
+or an index file (
+.B .ndx
+)
and prints out useful information about them.
option), or a pair of energy files (using the
.B -e2
option).
+
+
+For free energy simulations the A and B state topology from one
+run input file can be compared with options
+.B -s1
+and
+.B -ab
+.
+
+
+In case the
+.B -m
+flag is given a LaTeX file will be written
+consisting a rough outline for a methods section for a paper.
.SH FILES
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-f2" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s1" " top1.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-s2" " top2.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-c" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-e" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-e2" " ener2.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
+.BI "-m" " doc.tex"
+.B Output, Opt.
+ LaTeX file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-vdwfac" " real" " 0.8"
+.BI "-vdwfac" " real" " 0.8 "
Fraction of sum of VdW radii used as warning cutoff
-.BI "-bonlo" " real" " 0.4"
+.BI "-bonlo" " real" " 0.4 "
Min. fract. of sum of VdW radii for bonded atoms
-.BI "-bonhi" " real" " 0.7"
+.BI "-bonhi" " real" " 0.7 "
Max. fract. of sum of VdW radii for bonded atoms
-.BI "-tol" " real" " 0.001"
+.BI "-tol" " real" " 0.001 "
Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)
+.BI "-[no]ab" "no "
+ Compare the A and B topology from one file
+
.BI "-lastener" " string" " "
Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.
-.TH gmxdump 1 "Mon 29 Aug 2005"
+.TH gmxdump 1 "Mon 22 Sep 2008"
.SH NAME
gmxdump
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3gmxdump\fP
.BI "-s" " topol.tpr "
.BI "-f" " traj.xtc "
.BI "-e" " ener.edr "
+.BI "-cp" " state.cpt "
+.BI "-om" " grompp.mdp "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-[no]nr" ""
checking your run input file in case of problems.
+When requesting to dump a topology file the program will dump
+the processed topology, since not all original information is maintained
+in tpr files.
.SH FILES
.BI "-s" " topol.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-e" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
+
+.BI "-cp" " state.cpt"
+.B Input, Opt.
+ Checkpoint file
+
+.BI "-om" " grompp.mdp"
+.B Output, Opt.
+ grompp input file with MD parameters
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]nr" " yes"
+.BI "-[no]nr" "yes "
Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)
-.TH grompp 1 "Mon 29 Aug 2005"
+.TH grompp 1 "Mon 22 Sep 2008"
.SH NAME
grompp
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3grompp\fP
.BI "-f" " grompp.mdp "
.BI "-r" " conf.gro "
.BI "-rb" " conf.gro "
.BI "-n" " index.ndx "
-.BI "-deshuf" " deshuf.ndx "
.BI "-p" " topol.top "
.BI "-pp" " processed.top "
.BI "-o" " topol.tpr "
.BI "-nice" " int "
.BI "-[no]v" ""
.BI "-time" " real "
-.BI "-np" " int "
-.BI "-[no]shuffle" ""
-.BI "-[no]sort" ""
.BI "-[no]rmvsbds" ""
-.BI "-load" " string "
.BI "-maxwarn" " int "
-.BI "-[no]check14" ""
+.BI "-[no]zero" ""
.BI "-[no]renum" ""
.SH DESCRIPTION
The gromacs preprocessor
only the atom types are used for generating interaction parameters.
-grompp calls the c-preprocessor to resolve includes, macros
-etcetera. To specify a macro-preprocessor other than /lib/cpp
-(such as m4)
+grompp calls a preprocessor to resolve includes, macros
+etcetera. By default we use the cpp in your path. To specify a different macro-preprocessor (e.g. m4) or alternative location
you can put a line in your parameter file specifying the path
-to that cpp. Specifying
+to that program. Specifying
.B -pp
will get the pre-processed
topology file written out.
.
-When preparing an input file for parallel
-.B mdrun
-it may
-be advantageous to partition the simulation system over the
-nodes in a way in which each node has a similar amount of
-work. The -shuffle option does just that. For a single protein
-in water this does not make a difference, however for a system where
-you have many copies of different molecules (e.g. liquid mixture
-or membrane/water system) the option is definitely a must.
-The output trajectories will also be shuffled.
-.B grompp
-writes
-an index file (option
-.B -deshuf
-) which can be used with
-
-.B trjconv
-to deshuffle the trajectories.
-
-
-A further optimization for parallel systems is the
-.B -sort
-
-option which sorts molecules according to coordinates. This must
-always be used in conjunction with
-.B -shuffle
-, however
-sorting also works when you have only one molecule type.
-
-
Using the
.B -morse
option grompp can convert the harmonic bonds
.BI "-c" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-r" " conf.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-rb" " conf.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
-.BI "-deshuf" " deshuf.ndx"
-.B Output, Opt.
- Index file
-
.BI "-p" " topol.top"
.B Input
Topology file
.BI "-o" " topol.tpr"
.B Output
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-t" " traj.trr"
.B Input, Opt.
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-e" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]v" " yes"
+.BI "-[no]v" "yes "
Be loud and noisy
-.BI "-time" " real" " -1"
+.BI "-time" " real" " -1 "
Take frame at or first after this time.
-.BI "-np" " int" " 1"
- Generate statusfile for nodes
-
-.BI "-[no]shuffle" " no"
- Shuffle molecules over nodes
-
-.BI "-[no]sort" " no"
- Sort molecules according to X coordinate
-
-.BI "-[no]rmvsbds" " yes"
+.BI "-[no]rmvsbds" "yes "
Remove constant bonded interactions with virtual sites
-.BI "-load" " string" " "
- Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node
-
-.BI "-maxwarn" " int" " 10"
- Number of warnings after which input processing stops
+.BI "-maxwarn" " int" " 0"
+ Number of allowed warnings during input processing
-.BI "-[no]check14" " no"
- Remove 1-4 interactions without Van der Waals
+.BI "-[no]zero" "no "
+ Set parameters for bonded interactions without defaults to zero instead of generating an error
-.BI "-[no]renum" " yes"
+.BI "-[no]renum" "yes "
Renumber atomtypes and minimize number of atomtypes
-.TH highway 1 "Mon 29 Aug 2005"
+.TH highway 1 "Mon 22 Sep 2008"
.SH NAME
highway
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3highway\fP
.BI "-f" " highway.dat "
Generic data file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
-.TH make_edi 1 "Mon 29 Aug 2005"
+.TH make_edi 1 "Mon 22 Sep 2008"
.SH NAME
make_edi
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3make_edi\fP
.BI "-f" " eigenvec.trr "
.BI "-mon" " string "
.BI "-linfix" " string "
.BI "-linacc" " string "
+.BI "-flood" " string "
.BI "-radfix" " string "
.BI "-radacc" " string "
.BI "-radcon" " string "
-.BI "-flood" " string "
.BI "-outfrq" " int "
.BI "-slope" " real "
.BI "-maxedsteps" " int "
.BI "-accdir" " string "
.BI "-radstep" " real "
.BI "-[no]restrain" ""
-.BI "-[no]hesse" ""
+.BI "-[no]hessian" ""
.BI "-[no]harmonic" ""
.SH DESCRIPTION
.B make_edi
-generates an ED-sampling input file to be used with mdrun
+generates an essential dynamics (ED) sampling input file to be used with mdrun
based on eigenvectors of a covariance matrix (
.B g_covar
) or from a
-Normal Modes anaysis (
+normal modes anaysis (
.B g_nmeig
).
-ED-sampling can be used to manipulate the position along collective coordinates
+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
the system to explore new regions along these collective coordinates. A number
to keep the position along a certain (set of) coordinate(s) fixed (
.B -linfix
),
-or to only monitor the projections of the positions, velocities and forces onto
-these coordinates(
+or to only monitor the projections of the positions onto
+these coordinates (
.B -mon
).
.B -mon
-: monitor projections of x, v and f onto selected eigenvectors.
+: monitor projections of the coordinates onto selected eigenvectors.
: perform acceptance radius contraction along selected eigenvectors
towards a target structure specified with
.B -tar
-.NOTE: each eigenvector can be selected only once.
+.
+
+NOTE: each eigenvector can be selected only once.
.B -outfrq
-: frequency (in steps) of writing out projections etc.
+: frequency (in steps) of writing out projections etc. to .edo file
+
.B -slope
before a new cycle is started.
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 (it would
-require much extra communication to fully parallelize the algorithms).
-Fortunately, however, a typical parallel protein simulation in gromacs has
-most or all protein coordinates on one processor (the master) and has only
-other atoms (solvent, lipid, ions etc) on the other processors. With such a
-setup, ED sampling will still work. If the atoms over which ED sampling should
-be performed are spread over multiple processors, a fatal error will result.
-
-All output of mdrun (specify with -eo) is written to a .edo file (some extra
-information is written to the log file of mdrun too, actually). The .edo format
-is a simple ASCII file that should be easy to parse with standard unix tools
-like awk. A script (parse_edo) can be downloaded from contribution section at
- www.gromacs.org to extract information from the
-.edo files for your convinience. In short, the header defines which information
-can be expected in the rest of the .edo file. After the header, per step the
-following information is present:
+(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.
-* the step number
+All output of mdrun (specify with -eo) is written to a .edo file. In the output
+file, per OUTFRQ step the following information is present:
-* RMSD (for atoms in fitting prior to calculating ED constr.)
-* projections of the positions onto selected eigenvectors
-
-* projections of the velocities onto selected eigenvectors
+* the step number
-* projections of the forces onto selected eigenvectors
+* 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 .edi files were concatenated
+first. The constraints are applied in the order they appear in the .edi file.)
+* RMSD (for atoms involved in fitting prior to calculating the ED constraints)
+* projections of the positions onto selected eigenvectors
-All projections are in the same order as in the header, so if you have e.g.
-2 groups (say one group over which acceptance radius expansion is performed,
-and another for which the projections are merely monitored) then you first
-get the position projections for each of the 2 groups, then the velocities
-and then the forces. Radii are not explicitly written to the .edo file, as
-they can be readily projected back from the positions. Alternatively, radii
-may be 'grepped from the log file.
with -flood 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
+by the covariance matrix. If you switch -restrain the potential is inverted and the structure
+is kept in that region.
-the origin is normally the average structure stored in the eigvec.trr file
-it can be changed with -ori to an arbitrary position in configurational space
-with -tau , -deltaF0 and -Eflnull you control the flooding strength
-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)
-deltaF0 is the flooding strength you want to reach after tau ps of simulation
-to use constant Efl set -tau to zero
+The origin is normally the average structure stored in the eigvec.trr file.
+It can be changed with -ori to an arbitrary position in configurational space.
+With -tau, -deltaF0 and -Eflnull 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).
+DeltaF0 is the flooding strength you want to reach after tau ps of simulation.
+To use constant Efl set -tau to zero.
-alpha 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 alpha1for restraining alpha1 can give you smaller width in the restraining potentialRESTART and FLOODING:
+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 alpha1.
+For restraining alpha1 can give you smaller width in the restraining potential.
+
+
+
+RESTART and FLOODING:
If you want to restart a crashed flooding simulation please find the values deltaF and Efl in
-the output file and write them with your texteditor into the .edi file under DELTA_F0 and EFL_NULL
+the output file and manually put them into the .edi file under DELTA_F0 and EFL_NULL.
.SH FILES
.BI "-f" " eigenvec.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-eig" " eigenval.xvg"
.B Input, Opt.
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-tar" " target.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-ori" " origin.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " sam.edi"
.B Output
ED sampling input
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-mon" " string" " "
- Indices of eigenvectors for projections of x, v and f (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91
+ Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91
.BI "-linfix" " string" " "
Indices of eigenvectors for fixed increment linear sampling
.BI "-linacc" " string" " "
Indices of eigenvectors for acceptance linear sampling
+.BI "-flood" " string" " "
+ Indices of eigenvectors for flooding
+
.BI "-radfix" " string" " "
Indices of eigenvectors for fixed increment radius expansion
.BI "-radcon" " string" " "
Indices of eigenvectors for acceptance radius contraction
-.BI "-flood" " string" " "
- Indices of eigenvectors for flooding
-
.BI "-outfrq" " int" " 100"
- freqency (in steps) of writing output in .edo file
+ Freqency (in steps) of writing output in .edo file
-.BI "-slope" " real" " 0"
- minimal slope in acceptance radius expamsion
+.BI "-slope" " real" " 0 "
+ Minimal slope in acceptance radius expansion
.BI "-maxedsteps" " int" " 0"
- max nr of steps per cycle
+ Max nr of steps per cycle
-.BI "-deltaF0" " real" " 150"
- target destabilization energy - used for flooding
+.BI "-deltaF0" " real" " 150 "
+ Target destabilization energy - used for flooding
-.BI "-deltaF" " real" " 0"
- start deltaF with this parameter - default 0, i.g. nonzero values only needed for restart
+.BI "-deltaF" " real" " 0 "
+ Start deltaF with this parameter - default 0, i.e. nonzero values only needed for restart
-.BI "-tau" " real" " 0.1"
- coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength
+.BI "-tau" " real" " 0.1 "
+ Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength
.BI "-eqsteps" " int" " 0"
- number of steps to run without any perturbations
+ Number of steps to run without any perturbations
-.BI "-Eflnull" " real" " 0"
- 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.
+.BI "-Eflnull" " real" " 0 "
+ 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.
-.BI "-T" " real" " 300"
- T is temperature, the value is needed if you want to do flooding
+.BI "-T" " real" " 300 "
+ T is temperature, the value is needed if you want to do flooding
-.BI "-alpha" " real" " 1"
- scale width of gaussian flooding potential with alpha2
+.BI "-alpha" " real" " 1 "
+ Scale width of gaussian flooding potential with alpha2
.BI "-linstep" " string" " "
Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! "1.0 2.3 5.1 -3.1")
.BI "-accdir" " string" " "
Directions for acceptance linear sampling - only sign counts! (put in quotes! "-1 +1 -1.1")
-.BI "-radstep" " real" " 0"
+.BI "-radstep" " real" " 0 "
Stepsize (nm/step) for fixed increment radius expansion
-.BI "-[no]restrain" " no"
- use the flooding potential with inverted sign - effects as quasiharmonic restraining potential
+.BI "-[no]restrain" "no "
+ Use the flooding potential with inverted sign - effects as quasiharmonic restraining potential
-.BI "-[no]hesse" " no"
- the eigenvectors and eigenvalues are from a Hesse matrix
+.BI "-[no]hessian" "no "
+ The eigenvectors and eigenvalues are from a Hessian matrix
-.BI "-[no]harmonic" " no"
- the eigenvalues are interpreted as spring constant
+.BI "-[no]harmonic" "no "
+ The eigenvalues are interpreted as spring constant
-.TH make_ndx 1 "Mon 29 Aug 2005"
+.TH make_ndx 1 "Mon 22 Sep 2008"
.SH NAME
make_ndx
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3make_ndx\fP
.BI "-f" " conf.gro "
.SH FILES
.BI "-f" " conf.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt., Mult.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
-.TH mdrun 1 "Mon 29 Aug 2005"
+.TH mdrun 1 "Mon 22 Sep 2008"
.SH NAME
mdrun
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3mdrun\fP
.BI "-s" " topol.tpr "
.BI "-o" " traj.trr "
.BI "-x" " traj.xtc "
+.BI "-cpi" " state.cpt "
+.BI "-cpo" " state.cpt "
.BI "-c" " confout.gro "
.BI "-e" " ener.edr "
.BI "-g" " md.log "
.BI "-field" " field.xvg "
.BI "-table" " table.xvg "
.BI "-tablep" " tablep.xvg "
+.BI "-tableb" " table.xvg "
.BI "-rerun" " rerun.xtc "
.BI "-tpi" " tpi.xvg "
+.BI "-tpid" " tpidist.xvg "
.BI "-ei" " sam.edi "
.BI "-eo" " sam.edo "
.BI "-j" " wham.gct "
.BI "-ffout" " gct.xvg "
.BI "-devout" " deviatie.xvg "
.BI "-runav" " runaver.xvg "
-.BI "-pi" " pull.ppa "
-.BI "-po" " pullout.ppa "
-.BI "-pd" " pull.pdo "
-.BI "-pn" " pull.ndx "
+.BI "-px" " pullx.xvg "
+.BI "-pf" " pullf.xvg "
.BI "-mtx" " nm.mtx "
.BI "-dn" " dipole.ndx "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-deffnm" " string "
.BI "-[no]xvgr" ""
-.BI "-np" " int "
-.BI "-nt" " int "
+.BI "-[no]pd" ""
+.BI "-dd" " vector "
+.BI "-npme" " int "
+.BI "-ddorder" " enum "
+.BI "-[no]ddcheck" ""
+.BI "-rdd" " real "
+.BI "-rcon" " real "
+.BI "-dlb" " enum "
+.BI "-dds" " real "
+.BI "-[no]sum" ""
.BI "-[no]v" ""
.BI "-[no]compact" ""
-.BI "-[no]sepdvdl" ""
-.BI "-[no]multi" ""
+.BI "-[no]seppot" ""
+.BI "-pforce" " real "
+.BI "-[no]reprod" ""
+.BI "-cpt" " real "
+.BI "-[no]append" ""
+.BI "-maxh" " real "
+.BI "-multi" " int "
.BI "-replex" " int "
.BI "-reseed" " int "
.BI "-[no]glas" ""
.SH DESCRIPTION
The mdrun program is the main computational chemistry engine
within GROMACS. Obviously, it performs Molecular Dynamics simulations,
-but it can also perform Brownian Dynamics and Langevin Dynamics
-as well as Conjugate Gradient or Steepest Descents energy minimization.
+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
builds a Hessian matrix from single conformation.
For usual Normal Modes-like calculations, make sure that
-the structure provided is properly energy-minimised.
+the structure provided is properly energy-minimized.
The generated matrix can be diagonalized by g_nmeig.
+
The mdrun program reads the run input file (
.B -s
-) and distributes the
-topology over nodes if needed. The coordinates are passed
-around, so that computations can begin.
-First a neighborlist is made, then the forces are computed.
-The forces are globally summed, and the velocities and
-positions are updated. If necessary shake is performed to constrain
-bond lengths and/or bond angles.
-Temperature and Pressure can be controlled using weak coupling to a
-bath.
-
-
-mdrun produces at least three output file, plus one log file
-(
+)
+and distributes the topology over nodes if needed.
+mdrun produces at least four output files.
+A single log file (
.B -g
-) per node.
+) is written, unless the option
+
+.B -seppot
+is used, in which case each node writes a log file.
The trajectory file (
.B -o
), contains coordinates, velocities and
The energy file (
.B -e
) contains energies, the temperature,
-pressure, etc, a lot of these things are also printed in the log file
-of node 0.
+pressure, etc, a lot of these things are also printed in the log file.
Optionally coordinates can be written to a compressed trajectory file
(
.B -x
).
-When running in parallel with PVM or an old version of MPI the
-
-.B -np
-option must be given to indicate the number of
-nodes.
-
-
The option
.B -dgdl
is only used when free energy perturbation is
turned on.
+When mdrun is started using MPI with more than 1 node, parallelization
+is used. By default domain decomposition is used, unless the
+.B -pd
+
+option is set, which selects particle decomposition.
+
+
+With domain decomposition, the spatial decomposition can be set
+with option
+.B -dd
+. By default mdrun 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
+.B -dlb
+,
+which can give a significant performance improvement,
+especially for inhomogeneous systems. The only disadvantage of
+dynamic load balancing is that runs are no longer binary reproducible,
+but in most cases this is not important.
+By default the dynamic load balancing is automatically turned on
+when the measured performance loss due to load imbalance is 5% or more.
+At low parallelization these are the only important options
+for domain decomposition.
+At high parallelization the options in the next two sections
+could be important for increasing the performace.
+
+
+
+When PME is used with domain decomposition, separate nodes can
+be assigned to do only the PME mesh calculation;
+this is computationally more efficient starting at about 12 nodes.
+The number of PME nodes is set with option
+.B -npme
+,
+this can not be more than half of the nodes.
+By default mdrun 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
+are written at the end of the log file.
+For good load balancing at high parallelization,
+npme should be divisible by the number of PME nodes
+
+
+
+This section lists all options that affect the domain decomposition.
+
+
+Option
+.B -rdd
+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
+cut-off distance always comes for free with the non-bonded communication.
+Atoms beyond the non-bonded cut-off are only communicated when they have
+missing bonded interactions; this means that the extra cost is minor
+and nearly indepedent of the value of
+.B -rdd
+.
+With dynamic load balancing option
+.B -rdd
+also sets
+the lower limit for the domain decomposition cell sizes.
+By default
+.B -rdd
+is determined by mdrun based on
+the initial coordinates. The chosen value will be a balance
+between interaction range and communication cost.
+
+
+When inter charge-group bonded interactions are beyond
+the bonded cut-off distance, mdrun 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
+.B -noddcheck
+.B .
+
+
+When constraints are present, option
+.B -rcon
+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
+in a conservative fashion. For high parallelization it can be useful
+to set the distance required for P-LINCS with the option
+.B -rcon
+.
+
+
+The
+.B -dds
+option sets the minimum allowed x, y and/or z scaling
+of the cells with dynamic load balancing. mdrun 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
+.B -dd
+)
+as well as for determining the number of grid pulses, which in turn
+sets the minimum allowed cell size. Under certain circumstances
+the value of
+.B -dds
+might need to be adjusted to account for
+high or low spatial inhomogeneity of the system.
+
+
+
+The option
+.B -nosum
+can be used to only sum the energies
+at every neighbor search step and energy output step.
+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 nstlist steps.
+With this option the energy file will not contain averages and
+fluctuations over all integration steps.
+
+
With
.B -rerun
an input trajectory can be given for which
option is used to pass mdrun
a formatted table with potential functions. The file is read from
either the current directory or from the GMXLIB directory.
-A number of preformatted tables are presented in the GMXLIB dir,
+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
normal Coulomb.
-When pair interactions are present a seperate table for pair interaction
+When pair interactions are present a separate table for pair interaction
functions is read using the
.B -tablep
option.
+When tabulated bonded functions are present in the topology,
+interaction functions are read using the
+.B -tableb
+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
+and finally the table number of the interaction type.
+
+
The options
.B -pi
,
With
.B -multi
multiple systems are simulated in parallel.
-As many (single node) input files are required as the number of nodes.
-The node number is appended to the run input and each output filename,
+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.tpr becomes topol0.tpr, topol1.tpr etc.
-The main use of this option is for NMR refinement: when distance
+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.
With
.B -replex
replica exchange is attempted every given number
-of steps. This option implies
+of steps. The number of replicas is set with the
.B -multi
-, see above.
+option,
+see 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
Finally some experimental algorithms can be tested when the
appropriate options have been given. Currently under
-investigation are: polarizibility, glass simulations
+investigation are: polarizability, glass simulations
and X-Ray bombardments.
+
+The option
+.B -pforce
+is useful when you suspect a simulation
+crashes due to too large forces. With this option coordinates and
+forces of atoms with a force larger than a certain value will
+be printed to stderr.
+
+
+
+Checkpoints containing the complete state of the system are written
+at regular intervals (option
+.B -cpt
+) to the file
+.B -cpo
+,
+unless option
+.B -cpt
+is set to -1.
+A simulation can be continued by reading the full state from file
+with option
+.B -cpi
+. 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 tpr file.
+
+
+
+With checkpointing you can also use the option
+.B -append
+to
+just continue writing to the previous output files. This is not
+enabled by default since it is potentially dangerous if you move files,
+but if you just leave all your files in place and restart mdrun with
+exactly the same command (with options
+.B -cpi
+and
+.B -append
+)
+the result will be the same as from a single run. The contents will
+be binary identical (unless you use dynamic load balancing),
+but for technical reasons there might be some extra energy frames when
+using checkpointing (necessary for restarts without appending).
+
+
+
+With option
+.B -maxh
+a simulation is terminated and a checkpoint
+file is written at the first neighbor search step where the run time
+exceeds
+.B -maxh
+*0.99 hours.
+
+
+
When mdrun receives a TERM signal, it will set nsteps to the current
-step plus one. When mdrun receives a USR1 signal, it will set nsteps
-to the next multiple of nstxout after the current step.
+step plus one. When mdrun receives a USR1 signal, 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
is sufficient, this signal should not be sent to mpirun or
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " traj.trr"
.B Output
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-x" " traj.xtc"
.B Output, Opt.
Compressed trajectory (portable xdr format)
+.BI "-cpi" " state.cpt"
+.B Input, Opt.
+ Checkpoint file
+
+.BI "-cpo" " state.cpt"
+.B Output, Opt.
+ Checkpoint file
+
.BI "-c" " confout.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-e" " ener.edr"
.B Output
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-g" " md.log"
.B Output
.B Input, Opt.
xvgr/xmgr file
+.BI "-tableb" " table.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
.BI "-rerun" " rerun.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-tpi" " tpi.xvg"
.B Output, Opt.
xvgr/xmgr file
+.BI "-tpid" " tpidist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-ei" " sam.edi"
.B Input, Opt.
ED sampling input
.B Output, Opt.
xvgr/xmgr file
-.BI "-pi" " pull.ppa"
-.B Input, Opt.
- Pull parameters
-
-.BI "-po" " pullout.ppa"
+.BI "-px" " pullx.xvg"
.B Output, Opt.
- Pull parameters
+ xvgr/xmgr file
-.BI "-pd" " pull.pdo"
+.BI "-pf" " pullf.xvg"
.B Output, Opt.
- Pull data output
-
-.BI "-pn" " pull.ndx"
-.B Input, Opt.
- Index file
+ xvgr/xmgr file
.BI "-mtx" " nm.mtx"
.B Output, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
.BI "-deffnm" " string" " "
Set the default filename for all file options
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-np" " int" " 1"
- Number of nodes, must be the same as used for grompp
+.BI "-[no]pd" "no "
+ Use particle decompostion
-.BI "-nt" " int" " 1"
- Number of threads to start on each node
+.BI "-dd" " vector" " 0 0 0"
+ Domain decomposition grid, 0 is optimize
+
+.BI "-npme" " int" " -1"
+ Number of separate nodes to be used for PME, -1 is guess
+
+.BI "-ddorder" " enum" " interleave"
+ DD node order:
+.B interleave
+,
+.B pp_pme
+or
+.B cartesian
-.BI "-[no]v" " no"
+
+.BI "-[no]ddcheck" "yes "
+ Check for all bonded interactions with DD
+
+.BI "-rdd" " real" " 0 "
+ The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates
+
+.BI "-rcon" " real" " 0 "
+ Maximum distance for P-LINCS (nm), 0 is estimate
+
+.BI "-dlb" " enum" " auto"
+ Dynamic load balancing (with DD):
+.B auto
+,
+.B no
+or
+.B yes
+
+
+.BI "-dds" " real" " 0.8 "
+ Minimum allowed dlb scaling of the DD cell size
+
+.BI "-[no]sum" "yes "
+ Sum the energies at every step
+
+.BI "-[no]v" "no "
Be loud and noisy
-.BI "-[no]compact" " yes"
+.BI "-[no]compact" "yes "
Write a compact log file
-.BI "-[no]sepdvdl" " no"
+.BI "-[no]seppot" "no "
Write separate V and dVdl terms for each interaction type and node to the log file(s)
-.BI "-[no]multi" " no"
- Do multiple simulations in parallel (only with -np 1)
+.BI "-pforce" " real" " -1 "
+ Print all forces larger than this (kJ/mol nm)
+
+.BI "-[no]reprod" "no "
+ Try to avoid optimizations that affect binary reproducibility
+
+.BI "-cpt" " real" " 15 "
+ Checkpoint interval (minutes)
+
+.BI "-[no]append" "no "
+ Append to previous output files when restarting from checkpoint
+
+.BI "-maxh" " real" " -1 "
+ Terminate after 0.99 times this time (hours)
+
+.BI "-multi" " int" " 0"
+ Do multiple simulations in parallel
.BI "-replex" " int" " 0"
Attempt replica exchange every steps
.BI "-reseed" " int" " -1"
Seed for replica exchange, -1 is generate a seed
-.BI "-[no]glas" " no"
+.BI "-[no]glas" "no "
Do glass simulation with special long range corrections
-.BI "-[no]ionize" " no"
+.BI "-[no]ionize" "no "
Do a simulation including the effect of an X-Ray bombardment on your system
-.TH mk_angndx 1 "Mon 29 Aug 2005"
+.TH mk_angndx 1 "Mon 22 Sep 2008"
.SH NAME
mk_angndx
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3mk_angndx\fP
.BI "-s" " topol.tpr "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-type" " enum "
+.BI "-[no]hyd" ""
.SH DESCRIPTION
mk_angndx makes an index file for calculation of
angle distributions etc. It uses a run input file (
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " angle.ndx"
.B Output
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Type of angle:
.B angle
,
-.B g96-angle
-,
.B dihedral
,
.B improper
-,
-.B ryckaert-bellemans
or
-.B phi-psi
+.B ryckaert-bellemans
+
+.BI "-[no]hyd" "yes "
+ Include angles with atoms with mass 1.5
-.TH ngmx 1 "Mon 29 Aug 2005"
+.TH ngmx 1 "Mon 22 Sep 2008"
.SH NAME
ngmx
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3ngmx\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
+.SH KNOWN PROBLEMS
\- Balls option does not work
\- Some times dumps core without a good reason
-.TH pdb2gmx 1 "Mon 29 Aug 2005"
+.TH pdb2gmx 1 "Mon 22 Sep 2008"
.SH NAME
pdb2gmx
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3pdb2gmx\fP
.BI "-f" " eiwit.pdb "
.BI "-[no]ss" ""
.BI "-[no]ter" ""
.BI "-[no]lys" ""
+.BI "-[no]arg" ""
.BI "-[no]asp" ""
.BI "-[no]glu" ""
+.BI "-[no]gln" ""
.BI "-[no]his" ""
.BI "-angle" " real "
.BI "-dist" " real "
.SH FILES
.BI "-f" " eiwit.pdb"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " conf.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-p" " topol.top"
.B Output
.BI "-q" " clean.pdb"
.B Output, Opt.
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]merge" " no"
+.BI "-[no]merge" "no "
Merge chains into one molecule definition
.BI "-ff" " string" " select"
.B f3c
-.BI "-[no]inter" " no"
- Set the next 6 options to interactive
+.BI "-[no]inter" "no "
+ Set the next 8 options to interactive
-.BI "-[no]ss" " no"
+.BI "-[no]ss" "no "
Interactive SS bridge selection
-.BI "-[no]ter" " no"
+.BI "-[no]ter" "no "
Interactive termini selection, iso charged
-.BI "-[no]lys" " no"
+.BI "-[no]lys" "no "
Interactive Lysine selection, iso charged
-.BI "-[no]asp" " no"
+.BI "-[no]arg" "no "
+ Interactive Arganine selection, iso charged
+
+.BI "-[no]asp" "no "
Interactive Aspartic Acid selection, iso charged
-.BI "-[no]glu" " no"
+.BI "-[no]glu" "no "
Interactive Glutamic Acid selection, iso charged
-.BI "-[no]his" " no"
+.BI "-[no]gln" "no "
+ Interactive Glutamine selection, iso neutral
+
+.BI "-[no]his" "no "
Interactive Histidine selection, iso checking H-bonds
-.BI "-angle" " real" " 135"
+.BI "-angle" " real" " 135 "
Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
-.BI "-dist" " real" " 0.3"
+.BI "-dist" " real" " 0.3 "
Maximum donor-acceptor distance for a H-bond (nm)
-.BI "-[no]una" " no"
+.BI "-[no]una" "no "
Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine
-.BI "-[no]ignh" " no"
+.BI "-[no]ignh" "no "
Ignore hydrogen atoms that are in the pdb file
-.BI "-[no]missing" " no"
+.BI "-[no]missing" "no "
Continue when atoms are missing, dangerous
-.BI "-[no]v" " no"
+.BI "-[no]v" "no "
Be slightly more verbose in messages
-.BI "-posrefc" " real" " 1000"
+.BI "-posrefc" " real" " 1000 "
Force constant for position restraints
.BI "-vsite" " enum" " none"
.B aromatics
-.BI "-[no]heavyh" " no"
+.BI "-[no]heavyh" "no "
Make hydrogen atoms heavy
-.BI "-[no]deuterate" " no"
+.BI "-[no]deuterate" "no "
Change the mass of hydrogens to 2 amu
-.TH protonate 1 "Mon 29 Aug 2005"
+.TH protonate 1 "Mon 22 Sep 2008"
.SH NAME
protonate
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3protonate\fP
.BI "-s" " topol.tpr "
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " protonated.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.TH tpbconv 1 "Mon 29 Aug 2005"
+.TH tpbconv 1 "Mon 22 Sep 2008"
.SH NAME
tpbconv
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3tpbconv\fP
.BI "-s" " topol.tpr "
.BI "-o" " tpxout.tpr "
.BI "-[no]h" ""
.BI "-nice" " int "
+.BI "-nsteps" " int "
+.BI "-runtime" " real "
.BI "-time" " real "
.BI "-extend" " real "
.BI "-until" " real "
.BI "-[no]zeroq" ""
-.BI "-[no]unconstrained" ""
+.BI "-[no]cont" ""
.SH DESCRIPTION
-tpbconv can edit run input files in three ways.
+tpbconv can edit run input files in four ways.
.B 1st.
-by creating a run input file
+by modifying the number of steps in a run input file
+with option
+.B -nsteps
+or option
+.B -runtime
+.
+
+
+
+.B 2st.
+(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.
-Note that a frame with coordinates and velocities is needed,
-which means that when you never write velocities, you can not use
-tpbconv and you have to start the run again from the beginning.
+This option is obsolete, since mdrun now writes and reads
+checkpoint files.
+Note 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.
-.B 2nd.
+.B 3nd.
by creating a tpx 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 3rd.
+.B 4rd.
by setting the charges of a specified group
to zero. This is useful when doing free energy estimates
-using the LIE (Linear Interactio Energy) method.
+using the LIE (Linear Interaction Energy) method.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-f" " traj.trr"
.B Input, Opt.
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-e" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " tpxout.tpr"
.B Output
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-time" " real" " -1"
+.BI "-nsteps" " int" " -1"
+ Change the number of steps
+
+.BI "-runtime" " real" " -1 "
+ Set the run time (ps)
+
+.BI "-time" " real" " -1 "
Continue from frame at this time (ps) instead of the last frame
-.BI "-extend" " real" " 0"
+.BI "-extend" " real" " 0 "
Extend runtime by this amount (ps)
-.BI "-until" " real" " 0"
+.BI "-until" " real" " 0 "
Extend runtime until this ending time (ps)
-.BI "-[no]zeroq" " no"
+.BI "-[no]zeroq" "no "
Set the charges of a group (from the index) to zero
-.BI "-[no]unconstrained" " yes"
- For a continuous trajectory, the constraints should not be solved before the first step (default)
+.BI "-[no]cont" "yes "
+ For exact continuation, the constraints should not be solved before the first step
-.TH trjcat 1 "Mon 29 Aug 2005"
+.TH trjcat 1 "Mon 22 Sep 2008"
.SH NAME
trjcat
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3trjcat\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input, Mult.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-o" " trajout.xtc"
.B Output, Mult.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-b" " time" " -1"
+.BI "-b" " time" " -1 "
First time to use (ps)
-.BI "-e" " time" " -1"
+.BI "-e" " time" " -1 "
Last time to use (ps)
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only write frame when t MOD dt = first time (ps)
.BI "-prec" " int" " 3"
Precision for .xtc and .gro writing in number of decimal places
-.BI "-[no]vel" " yes"
+.BI "-[no]vel" "yes "
Read and write velocities if possible
-.BI "-[no]settime" " no"
+.BI "-[no]settime" "no "
Change starting time interactively
-.BI "-[no]sort" " yes"
+.BI "-[no]sort" "yes "
Sort trajectory files (not frames)
-.BI "-[no]keeplast" " no"
+.BI "-[no]keeplast" "no "
keep overlapping frames at end of trajectory
-.BI "-[no]cat" " no"
+.BI "-[no]cat" "no "
do not discard double time frames
-.TH trjconv 1 "Mon 29 Aug 2005"
+.TH trjconv 1 "Mon 22 Sep 2008"
.SH NAME
trjconv
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3trjconv\fP
.BI "-f" " traj.xtc "
.BI "-timestep" " time "
.BI "-pbc" " enum "
.BI "-ur" " enum "
-.BI "-center" " enum "
+.BI "-[no]center" ""
+.BI "-boxcenter" " enum "
.BI "-box" " vector "
+.BI "-trans" " vector "
.BI "-shift" " vector "
.BI "-fit" " enum "
.BI "-ndec" " int "
.BI "-[no]app" ""
.BI "-split" " time "
.BI "-[no]sep" ""
+.BI "-nzero" " int "
.BI "-[no]ter" ""
.BI "-dropunder" " real "
.BI "-dropover" " real "
select a subset of atoms
.B 3.
-remove periodicity from molecules
+change the periodicity representation
.B 4.
treatment:
*
-.B whole
-puts the atoms in the box and then makes
-broken molecules whole (a run input file is required).
-Atom number 1 of each molecule will be inside the box.
+.B mol
+puts the center of mass of molecules in the box.
*
-.B com
-puts the center of mass of all
-.I residues
-
-in the box. Not that this can break molecules that consist of
-more than one residue (e.g. proteins).
+.B res
+puts the center of mass of residues in the box.
*
-.B inbox
+.B atom
puts all the atoms in the box.
*
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
results if you in fact have a cluster. Luckily that can be checked
-afterwards using a trajectory viewer.
+afterwards using a trajectory viewer. Note also that if your molecules
+are broken this will not work either.
-
-.B -pbc
-is ignored when
-.B -fit
-or
-.B -pfit
-is set,
-in that case molecules will be made whole.
+*
+.B whole
+only makes broken molecules whole.
Option
.B -ur
sets the unit cell representation for options
-.B whole
+.B mol
+,
+.B res
and
-.B inbox
+.B atom
of
.B -pbc
.
is
.B tric
(see below), unless the option
-.B -center
+.B -boxcenter
is set differently.
.B -center
centers the system in the box. The user can
select the group which is used to determine the geometrical center.
-The center options are:
+Option
+.B -boxcenter
+sets the location of the center of the box
+for options
+.B -pbc
+and
+.B -center
+. The center options are:
.B tric
: half of the sum of the box vectors,
.B zero
: zero.
Use option
-.B -pbc whole
+.B -pbc mol
in addition to
.B -center
when you
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-o" " trajout.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-skip" " int" " 1"
Only write every nr-th frame
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only write frame when t MOD dt = first time (ps)
-.BI "-dump" " time" " -1"
+.BI "-dump" " time" " -1 "
Dump frame nearest specified time (ps)
-.BI "-t0" " time" " 0"
+.BI "-t0" " time" " 0 "
Starting time (ps) (default: don't change)
-.BI "-timestep" " time" " 0"
+.BI "-timestep" " time" " 0 "
Change time step between input frames (ps)
.BI "-pbc" " enum" " none"
PBC treatment (see help text for full description):
.B none
,
-.B whole
+.B mol
+,
+.B res
,
-.B inbox
+.B atom
,
.B nojump
,
.B cluster
or
-.B com
+.B whole
.BI "-ur" " enum" " rect"
.B compact
-.BI "-center" " enum" " no"
- Center atoms in box:
-.B no
-,
+.BI "-[no]center" "no "
+ Center atoms in box
+
+.BI "-boxcenter" " enum" " tric"
+ Center for -pbc and -center:
.B tric
,
.B rect
.BI "-box" " vector" " 0 0 0"
Size for new cubic box (default: read from input)
+.BI "-trans" " vector" " 0 0 0"
+ All coordinates will be translated by trans. This can advantageously be combined with -pbc mol -ur compact.
+
.BI "-shift" " vector" " 0 0 0"
All coordinates will be shifted by framenr*shift
,
.B rot+trans
,
+.B rotxy+transxy
+,
.B translation
or
.B progressive
.BI "-ndec" " int" " 3"
Precision for .xtc and .gro writing in number of decimal places
-.BI "-[no]vel" " yes"
+.BI "-[no]vel" "yes "
Read and write velocities if possible
-.BI "-[no]force" " no"
+.BI "-[no]force" "no "
Read and write forces if possible
-.BI "-trunc" " time" " -1"
+.BI "-trunc" " time" " -1 "
Truncate input trj file after this time (ps)
.BI "-exec" " string" " "
Execute command for every output frame with the frame number as argument
-.BI "-[no]app" " no"
+.BI "-[no]app" "no "
Append output
-.BI "-split" " time" " 0"
+.BI "-split" " time" " 0 "
Start writing new file when t MOD split = first time (ps)
-.BI "-[no]sep" " no"
+.BI "-[no]sep" "no "
Write each frame to a separate .gro, .g96 or .pdb file
-.BI "-[no]ter" " no"
+.BI "-nzero" " int" " 0"
+ Prepend file number in case you use the -sep flag with this number of zeroes
+
+.BI "-[no]ter" "no "
Use 'TER' in pdb file as end of frame in stead of default 'ENDMDL'
-.BI "-dropunder" " real" " 0"
+.BI "-dropunder" " real" " 0 "
Drop all frames below this value
-.BI "-dropover" " real" " 0"
+.BI "-dropover" " real" " 0 "
Drop all frames above this value
-.TH trjorder 1 "Mon 29 Aug 2005"
+.TH trjorder 1 "Mon 22 Sep 2008"
.SH NAME
trjorder
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3trjorder\fP
.BI "-f" " traj.xtc "
with any Gromacs program to analyze the n closest waters.
+
If the output file is a pdb file, the distance to the reference target
will be stored in the B-factor field in order to color with e.g. rasmol.
+
+
+
+With option
+.B -nshell
+the number of molecules within a shell
+of radius
+.B -r
+around the refernce group are printed.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
.BI "-o" " ordered.xtc"
-.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+.B Output, Opt.
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-nshell" " nshell.xvg"
.B Output, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-na" " int" " 3"
.BI "-da" " int" " 1"
Atom used for the distance calculation
-.BI "-[no]com" " no"
+.BI "-[no]com" "no "
Use the distance to the center of mass of the reference group
-.BI "-r" " real" " 0"
+.BI "-r" " real" " 0 "
Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein
-.TH wheel 1 "Mon 29 Aug 2005"
+.TH wheel 1 "Mon 22 Sep 2008"
.SH NAME
wheel
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3wheel\fP
.BI "-f" " nnnice.dat "
Encapsulated PostScript (tm) file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
.BI "-r0" " int" " 1"
The first residue number in the sequence
-.BI "-rot0" " real" " 0"
+.BI "-rot0" " real" " 0 "
Rotate around an angle initially (90 degrees makes sense)
.BI "-T" " string" " "
Plot a title in the center of the wheel (must be shorter than 10 characters, or it will overwrite the wheel)
-.BI "-[no]nn" " yes"
+.BI "-[no]nn" "yes "
Toggle numbers
-.TH x2top 1 "Mon 29 Aug 2005"
+.TH x2top 1 "Mon 22 Sep 2008"
.SH NAME
x2top
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3x2top\fP
.BI "-f" " conf.gro "
.BI "-r" " out.rtp "
.BI "-[no]h" ""
.BI "-nice" " int "
-.BI "-scale" " real "
.BI "-ff" " string "
+.BI "-[no]v" ""
.BI "-nexcl" " int "
.BI "-[no]H14" ""
.BI "-[no]alldih" ""
.BI "-[no]pairs" ""
.BI "-name" " string "
.BI "-[no]pbc" ""
+.BI "-[no]pdbq" ""
.BI "-[no]param" ""
.BI "-[no]round" ""
.BI "-kb" " real "
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " out.top"
.B Output, Opt.
Residue Type file used by pdb2gmx
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-scale" " real" " 1.1"
- Scaling factor for bonds with unknown atom types relative to atom type O
+.BI "-ff" " string" " oplsaa"
+ Force field for your simulation. Type "select" for interactive selcection.
-.BI "-ff" " string" " select"
- Select the force field for your simulation.
+.BI "-[no]v" "no "
+ Generate verbose output in the top file.
.BI "-nexcl" " int" " 3"
Number of exclusions
-.BI "-[no]H14" " yes"
+.BI "-[no]H14" "yes "
Use 3rd neighbour interactions for hydrogen atoms
-.BI "-[no]alldih" " no"
+.BI "-[no]alldih" "no "
Generate all proper dihedrals
-.BI "-[no]remdih" " no"
+.BI "-[no]remdih" "no "
Remove dihedrals on the same bond as an improper
-.BI "-[no]pairs" " yes"
+.BI "-[no]pairs" "yes "
Output 1-4 interactions (pairs) in topology file
.BI "-name" " string" " ICE"
Name of your molecule
-.BI "-[no]pbc" " yes"
+.BI "-[no]pbc" "yes "
Use periodic boundary conditions.
-.BI "-[no]param" " no"
+.BI "-[no]pdbq" "no "
+ Use the B-factor supplied in a pdb file for the atomic charges
+
+.BI "-[no]param" "yes "
Print parameters in the output
-.BI "-[no]round" " yes"
+.BI "-[no]round" "yes "
Round off measured values
.BI "-kb" " real" " 400000"
Bonded force constant (kJ/mol/nm2)
-.BI "-kt" " real" " 400"
+.BI "-kt" " real" " 400 "
Angle force constant (kJ/mol/rad2)
-.BI "-kp" " real" " 5"
+.BI "-kp" " real" " 5 "
Dihedral angle force constant (kJ/mol/rad2)
+.SH KNOWN PROBLEMS
\- The atom type selection is primitive. Virtually no chemical knowledge is used
\- Periodic boundary conditions screw up the bonding
-.TH xpm2ps 1 "Mon 29 Aug 2005"
+.TH xpm2ps 1 "Mon 22 Sep 2008"
.SH NAME
xpm2ps
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3xpm2ps\fP
.BI "-f" " root.xpm "
.BI "-[no]yonce" ""
.BI "-legend" " enum "
.BI "-diag" " enum "
-.BI "-combine" " enum "
.BI "-size" " real "
.BI "-bx" " real "
.BI "-by" " real "
.BI "-skip" " int "
.BI "-[no]zeroline" ""
.BI "-legoffset" " int "
+.BI "-combine" " enum "
+.BI "-cmin" " real "
+.BI "-cmax" " real "
.SH DESCRIPTION
xpm2ps makes a beautiful color plot of an XPixelMap file.
Labels and axis can be displayed, when they are supplied
.B -diag
to
.B none
-. With
-
-.B -combine
-an alternative operation can be selected to combine
-the matrices. In this case, a new color map will be generated with
+.
+In this case, a new color map will be generated with
a red gradient for negative numbers and a blue for positive.
-
-
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
+.B -combine
+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
+.B -cmin
+and
+.B -cmax
+.
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]frame" " yes"
+.BI "-[no]frame" "yes "
Display frame, ticks, labels, title and legend
.BI "-title" " enum" " top"
.B none
-.BI "-[no]yonce" " no"
+.BI "-[no]yonce" "no "
Show y-label only once
.BI "-legend" " enum" " both"
.B none
-.BI "-combine" " enum" " halves"
- Combine two matrices:
-.B halves
-,
-.B add
-,
-.B sub
-,
-.B mult
-or
-.B div
-
-
-.BI "-size" " real" " 400"
+.BI "-size" " real" " 400 "
Horizontal size of the matrix in ps units
-.BI "-bx" " real" " 0"
+.BI "-bx" " real" " 0 "
Element x-size, overrides -size (also y-size when -by is not set)
-.BI "-by" " real" " 0"
+.BI "-by" " real" " 0 "
Element y-size
.BI "-rainbow" " enum" " no"
.BI "-skip" " int" " 1"
only write out every nr-th row and column
-.BI "-[no]zeroline" " no"
+.BI "-[no]zeroline" "no "
insert line in xpm matrix where axis label is zero
.BI "-legoffset" " int" " 0"
Skip first N colors from xpm file for the legend
+.BI "-combine" " enum" " halves"
+ Combine two matrices:
+.B halves
+,
+.B add
+,
+.B sub
+,
+.B mult
+or
+.B div
+
+
+.BI "-cmin" " real" " 0 "
+ Minimum for combination output
+
+.BI "-cmax" " real" " 0 "
+ Maximum for combination output
+
-.TH xrama 1 "Mon 29 Aug 2005"
+.TH xrama 1 "Mon 22 Sep 2008"
.SH NAME
xrama
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3xrama\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff