g_bond.1 g_dyndom.1 g_nmeig.1 g_sorient.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_energy.1 g_order.1 g_traj.1 mk_angndx.1 \
+ g_densmap.1 g_sham.1 make_edi.1
EXTRA_DIST = ${man_MANS}
\ No newline at end of file
-.TH anadock 1 "Sun 25 Jan 2004"
+.TH anadock 1 "Mon 29 Aug 2005"
.SH NAME
anadock
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3anadock\fP
.BI "-f" " eiwit.pdb "
.BI "-g" " anadock.log "
.BI "-[no]h" ""
.BI "-nice" " int "
+.BI "-[no]xvgr" ""
.BI "-[no]free" ""
.BI "-[no]rms" ""
.BI "-cutoff" " real "
.BI "-nice" " int" " 0"
Set the nicelevel
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]free" " no"
Use Free energy estimate from autodock for sorting the classes
-.TH cdist 1 "Sun 25 Jan 2004"
+.TH cdist 1 "Mon 29 Aug 2005"
.SH NAME
cdist
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3cdist\fP
.BI "-s" " topol.tpr "
-.TH disco 1 "Sun 25 Jan 2004"
+.TH disco 1 "Mon 29 Aug 2005"
.SH NAME
disco
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3disco\fP
.BI "-g" " disco.log "
-.TH do_dssp 1 "Sun 25 Jan 2004"
+.TH do_dssp 1 "Mon 29 Aug 2005"
.SH NAME
do_dssp
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3do_dssp\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-sss" " string "
.SH DESCRIPTION
do_dssp
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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
-.TH editconf 1 "Sun 25 Jan 2004"
+.TH editconf 1 "Mon 29 Aug 2005"
.SH NAME
editconf
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3editconf\fP
.BI "-f" " conf.gro "
.BI "-n" " index.ndx "
.BI "-o" " out.gro "
+.BI "-mead" " mead.pqr "
.BI "-bf" " bfact.dat "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-density" " real "
.BI "-[no]vol" ""
.BI "-[no]pbc" ""
-.BI "-[no]mead" ""
.BI "-[no]grasp" ""
.BI "-rvdw" " real "
+.BI "-sig56" " real "
+.BI "-[no]vdwread" ""
.BI "-[no]atom" ""
.BI "-[no]legend" ""
.BI "-label" " string "
.B -rotate
rotates the coordinates and velocities.
+
+
+
.B -princ
aligns the principal axes of the system along the
coordinate axes, this may allow you to decrease the box volume,
but beware that molecules can rotate significantly in a nanosecond.
+
Scaling is applied before any of the other operations are
performed. Boxes can be scaled to give a certain density (option
-The program can optionally rotate the solute molecule to align the
-molecule along its principal axes (
-.B -rotate
-)
-
-
-
When writing
.B .pdb
files, B-factors can be
-With the option -mead a special pdb file for the MEAD electrostatics
+With the option -mead a special pdb (pqr) file for the MEAD electrostatics
program (Poisson-Boltzmann solver) can be made. A further prerequisite
is that the input file is a run input file.
The B-factor field is then filled with the Van der Waals radius
a cubic box with the corners cut off (such as Gromos) use:
-.B editconf -f in -rotate 0 -45 -35.264 -bt o -box veclen -o out
+.B editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out
where
Index file
.BI "-o" " out.gro"
-.B Output
+.B Output, Opt.
Generic structure: gro g96 pdb xml
+.BI "-mead" " mead.pqr"
+.B Output, Opt.
+ Coordinate file for MEAD
+
.BI "-bf" " bfact.dat"
.B Input, Opt.
Generic data file
.BI "-[no]pbc" " no"
Remove the periodicity (make molecule whole again)
-.BI "-[no]mead" " no"
- Store the charge of the atom in the occupancy field and the radius of the atom in the B-factor field
-
.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"
- Default Van der Waals radius if one can not be found in the database
+ 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"
+ Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
+
+.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"
Force B-factor attachment per atom
-.TH eneconv 1 "Sun 25 Jan 2004"
+.TH eneconv 1 "Mon 29 Aug 2005"
.SH NAME
eneconv
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3eneconv\fP
.BI "-f" " ener.edr "
-.TH ffscan 1 "Sun 25 Jan 2004"
+.TH ffscan 1 "Mon 29 Aug 2005"
.SH NAME
ffscan
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3ffscan\fP
.BI "-s" " topol.tpr "
.BI "-o" " junk.trr "
.BI "-[no]h" ""
.BI "-nice" " int "
+.BI "-[no]xvgr" ""
.BI "-tol" " real "
.BI "-fmax" " real "
.BI "-[no]comb" ""
.BI "-nice" " int" " 19"
Set the nicelevel
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-tol" " real" " 0.1"
Energy tolerance (kJ/mol) (zero means everything is printed)
-.TH g_anaeig 1 "Sun 25 Jan 2004"
+.TH g_anaeig 1 "Mon 29 Aug 2005"
.SH NAME
g_anaeig
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_anaeig\fP
.BI "-v" " eigenvec.trr "
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-first" " int "
.BI "-last" " int "
.BI "-skip" " int "
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-first" " int" " 1"
First eigenvector for analysis (-1 is select)
-.TH g_analyze 1 "Sun 25 Jan 2004"
+.TH g_analyze 1 "Mon 29 Aug 2005"
.SH NAME
g_analyze
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_analyze\fP
.BI "-f" " graph.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]time" ""
.BI "-b" " real "
.BI "-e" " real "
.BI "-[no]d" ""
.BI "-bw" " real "
.BI "-errbar" " enum "
+.BI "-[no]integrate" ""
+.BI "-aver_start" " real "
+.BI "-[no]xydy" ""
.BI "-filter" " real "
.BI "-[no]power" ""
.BI "-[no]subav" ""
These errors are plotted as a function of the block size.
Also an analytical block average curve is plotted, assuming
that the autocorrelation is a sum of two exponentials.
-The analytical curve for the block average BA is:
+The analytical curve for the block average is:
-BA(t) = sigma sqrt(2/T ( a (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +
+f(t) = sigma sqrt(2/T ( a (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +
- (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),
+ (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),
where T is the total time.
-a, tau1 and tau2 are obtained by fitting BA(t) to the calculated block
-average.
+a, tau1 and tau2 are obtained by fitting f2(t) to error2.
When the actual block average is very close to the analytical curve,
the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).
+The complete derivation is given in
+B. Hess, J. Chem. Phys. 116:209-217, 2002.
Option
.BI "-[no]h" " no"
Print help info and quit
-.BI "-nice" " int" " 19"
+.BI "-nice" " int" " 0"
Set the nicelevel
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]time" " yes"
Expect a time in the input
.B 90
+.BI "-[no]integrate" " no"
+ Integrate data function(s) numerically using trapezium rule
+
+.BI "-aver_start" " real" " 0"
+ Start averaging the integral from here
+
+.BI "-[no]xydy" " no"
+ Interpret second data set as error in the y values for integrating
+
.BI "-filter" " real" " 0"
Print the high-frequency fluctuation after filtering with a cosine filter of length
-.TH g_angle 1 "Sun 25 Jan 2004"
+.TH g_angle 1 "Mon 29 Aug 2005"
.SH NAME
g_angle
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_angle\fP
.BI "-f" " traj.xtc "
.BI "-ot" " dihtrans.xvg "
.BI "-oh" " trhisto.xvg "
.BI "-oc" " dihcorr.xvg "
+.BI "-or" " traj.trr "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-type" " enum "
.BI "-[no]all" ""
.BI "-binwidth" " real "
It should be noted that the indexfile should contain
atom-triples for angles or atom-quadruplets for dihedrals.
If this is not the case, the program will crash.
+
+
+With option
+.B -or
+a trajectory file is dumped containing cos andsin of selected dihedral angles which subsequently can be used as
+input for a PCA analysis using
+.B g_covar
+.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.B Output, Opt.
xvgr/xmgr file
+.BI "-or" " traj.trr"
+.B Output, Opt.
+ Trajectory in portable xdr format
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-type" " enum" " angle"
Type of angle to analyse:
.B angle
-.TH g_bond 1 "Sun 25 Jan 2004"
+.TH g_bond 1 "Mon 29 Aug 2005"
.SH NAME
g_bond
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_bond\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-blen" " real "
.BI "-tol" " real "
.BI "-[no]aver" ""
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-blen" " real" " -1"
Bond length. By default length of first bond
-.TH g_bundle 1 "Sun 25 Jan 2004"
+.TH g_bundle 1 "Mon 29 Aug 2005"
.SH NAME
g_bundle
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_bundle\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-tu" " enum "
+.BI "-[no]xvgr" ""
.BI "-na" " int "
.BI "-[no]z" ""
.SH DESCRIPTION
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B h
+.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
-.TH g_chi 1 "Sun 25 Jan 2004"
+.TH g_chi 1 "Mon 29 Aug 2005"
.SH NAME
g_chi
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_chi\fP
.BI "-s" " conf.gro "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-r0" " int "
.BI "-[no]phi" ""
.BI "-[no]psi" ""
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-r0" " int" " 1"
starting residue
-.TH g_cluster 1 "Sun 25 Jan 2004"
+.TH g_cluster 1 "Mon 29 Aug 2005"
.SH NAME
g_cluster
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_cluster\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]dista" ""
.BI "-nlevels" " int "
-.BI "-keepfree" " int "
.BI "-cutoff" " real "
.BI "-[no]fit" ""
.BI "-max" " real "
can be used to define the distance between structures.
-full linkage: add a structure to a cluster when its distance to any
+single linkage: add a structure to a cluster when its distance to any
element of the cluster is less than
.B cutoff
.
When the clustering algorithm assigns each structure to exactly one
-cluster (full linkage, Jarvis Patrick and gromos) and a trajectory
+cluster (single linkage, Jarvis Patrick and gromos) and a trajectory
file is supplied, the structure with
the smallest average distance to the others or the average structure
or all structures for each cluster will be written to a trajectory
.B -o
writes the RMSD values in the upper left half of the matrix
and a graphical depiction of the clusters in the lower right half
-(depends on
-.B -max
-and
-.B -keepfree
-).
+When
+.B -minstruct
+= 1 the graphical depiction is black
+when two structures are in the same cluster.
+When
+.B -minstruct
+ 1 different colors will be used for each
+cluster.
.B -g
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]dista" " no"
Use RMSD of distances instead of RMS deviation
.BI "-nlevels" " int" " 40"
Discretize RMSD matrix in levels
-.BI "-keepfree" " int" " -4"
- if 0 levels not to use when coloring clusters; if 0 nlevels/-keepfree+1 levels will not be used
-
.BI "-cutoff" " real" " 0.1"
RMSD cut-off (nm) for two structures to be neighbor
-.TH g_clustsize 1 "Sun 25 Jan 2004"
+.TH g_clustsize 1 "Mon 29 Aug 2005"
.SH NAME
g_clustsize
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_clustsize\fP
.BI "-f" " traj.xtc "
.BI "-mc" " maxclust.xvg "
.BI "-ac" " avclust.xvg "
.BI "-hc" " histo-clust.xvg "
+.BI "-temp" " temp.xvg "
+.BI "-mcn" " maxclust.ndx "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-cut" " real "
.BI "-[no]mol" ""
+.BI "-[no]pbc" ""
.BI "-nskip" " int "
.BI "-nlevels" " int "
+.BI "-ndf" " int "
.BI "-rgblo" " vector "
.BI "-rgbhi" " vector "
.SH DESCRIPTION
molecules rather than atoms, which allows clustering of large molecules.
In this case an index file would still contain atom numbers
or your calculcation will die with a SEGV.
+
+
+When velocities are present in your trajectory, the temperature of
+the largest cluster will be printed in a separate xvg file assuming
+that the particles are free to move. If you are using constraints,
+please correct the temperature. For instance water simulated with SHAKE
+or SETTLE will yield a temperature that is 1.5 times too low. You can
+compensate for this with the -ndf option. Remember to take the removal
+of center of mass motion into account.
+
+
+The
+.B -mc
+option will produce an index file containing the
+atom numbers of the largest cluster.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.B Output
xvgr/xmgr file
+.BI "-temp" " temp.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-mcn" " maxclust.ndx"
+.B Output, Opt.
+ Index file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-cut" " real" " 0.35"
Largest distance (nm) to be considered in a cluster
.BI "-[no]mol" " no"
Cluster molecules rather than atoms (needs tpr file)
+.BI "-[no]pbc" " yes"
+ Use periodic boundary conditions
+
.BI "-nskip" " int" " 0"
Number of frames to skip between writing
.BI "-nlevels" " int" " 20"
Number of levels of grey in xpm output
+.BI "-ndf" " int" " -1"
+ Number of degrees of freedom of the entire system for temperature calculation. If not set the number of atoms times three is used.
+
.BI "-rgblo" " vector" " 1 1 0"
RGB values for the color of the lowest occupied cluster size
-.TH g_confrms 1 "Sun 25 Jan 2004"
+.TH g_confrms 1 "Mon 29 Aug 2005"
.SH NAME
g_confrms
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_confrms\fP
.BI "-f1" " conf1.gro "
.BI "-nice" " int "
.BI "-[no]w" ""
.BI "-[no]one" ""
+.BI "-[no]mw" ""
.BI "-[no]pbc" ""
.BI "-[no]fit" ""
.BI "-[no]name" ""
.BI "-[no]one" " no"
Only write the fitted structure to file
+.BI "-[no]mw" " yes"
+ Mass-weighted fitting and RMSD
+
.BI "-[no]pbc" " no"
Try to make molecules whole again
-.TH g_covar 1 "Sun 25 Jan 2004"
+.TH g_covar 1 "Mon 29 Aug 2005"
.SH NAME
g_covar
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_covar\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-tu" " enum "
+.BI "-[no]xvgr" ""
.BI "-[no]fit" ""
.BI "-[no]ref" ""
.BI "-[no]mwa" ""
.BI "-last" " int "
+.BI "-[no]pbc" ""
.SH DESCRIPTION
.B g_covar
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B h
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]fit" " yes"
Fit to a reference structure
.BI "-last" " int" " -1"
Last eigenvector to write away (-1 is till the last)
+.BI "-[no]pbc" " yes"
+ Apply corrections for periodic boundary conditions
+
-.TH g_density 1 "Sun 25 Jan 2004"
+.TH g_density 1 "Mon 29 Aug 2005"
.SH NAME
g_density
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_density\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-d" " string "
.BI "-sl" " int "
.BI "-[no]number" ""
.BI "-[no]ed" ""
.BI "-[no]count" ""
+.BI "-ng" " int "
+.BI "-[no]symm" ""
+.BI "-[no]center" ""
.SH DESCRIPTION
Compute partial densities across the box, using an index file. Densities
in kg/m3, number densities or electron densities can be
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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 "-[no]count" " no"
Only count atoms in slices, no densities. Hydrogens are not counted
+.BI "-ng" " int" " 0"
+ Number of groups to compute densities of
+
+.BI "-[no]symm" " no"
+ Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
+
+.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.
+
\- 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_dielectric 1 "Sun 25 Jan 2004"
+.TH g_dielectric 1 "Mon 29 Aug 2005"
.SH NAME
g_dielectric
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_dielectric\fP
.BI "-f" " Mtot.xvg "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]fft" ""
.BI "-[no]x1" ""
.BI "-eint" " real "
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]fft" " no"
use fast fourier transform for correlation function
-.TH g_dih 1 "Sun 25 Jan 2004"
+.TH g_dih 1 "Mon 29 Aug 2005"
.SH NAME
g_dih
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_dih\fP
.BI "-f" " traj.xtc "
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
.BI "-mult" " int" " -1"
mulitiplicity for dihedral angles (by default read from topology)
-\- should not ask for number of frames
-
-.TH g_dipoles 1 "Sun 25 Jan 2004"
+.TH g_dipoles 1 "Mon 29 Aug 2005"
.SH NAME
g_dipoles
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_dipoles\fP
.BI "-enx" " ener.edr "
.BI "-d" " dipdist.xvg "
.BI "-c" " dipcorr.xvg "
.BI "-g" " gkr.xvg "
+.BI "-adip" " adip.xvg "
+.BI "-dip3d" " dip3d.xvg "
+.BI "-cos" " cosaver.xvg "
.BI "-q" " quadrupole.xvg "
+.BI "-slab" " slab.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-mu" " real "
.BI "-mumax" " real "
.BI "-epsilonRF" " real "
.BI "-skip" " int "
.BI "-temp" " real "
.BI "-[no]avercorr" ""
+.BI "-[no]pairs" ""
+.BI "-axis" " string "
+.BI "-sl" " int "
.BI "-gkratom" " int "
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.B Output, Opt.
xvgr/xmgr file
+.BI "-adip" " adip.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-dip3d" " dip3d.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-cos" " cosaver.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-q" " quadrupole.xvg"
.B Output, Opt.
xvgr/xmgr file
+.BI "-slab" " slab.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-mu" " real" " -1"
dipole of a single molecule (in Debye)
.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"
+ Calculate |cos theta| between all pairs of molecules. May be slow
+
+.BI "-axis" " string" " Z"
+ Take the normal on the computational box in direction X, Y or Z.
+
+.BI "-sl" " int" " 10"
+ Divide the box in nr slices.
+
.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
-.TH g_disre 1 "Sun 25 Jan 2004"
+.TH g_disre 1 "Mon 29 Aug 2005"
.SH NAME
g_disre
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_disre\fP
.BI "-s" " topol.tpr "
.BI "-l" " disres.log "
.BI "-n" " viol.ndx "
.BI "-q" " viol.pdb "
+.BI "-c" " clust.ndx "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-ntop" " int "
.SH DESCRIPTION
g_disre computes violations of distance restraints.
.B -q
flag is given a pdb file coloured by the
amount of average violations.
+
+
+When the
+.B -c
+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
+averaging algorithm and print them in the log file.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
.B Output, Opt.
Protein data bank file
+.BI "-c" " clust.ndx"
+.B Input, Opt.
+ Index file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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
-.TH g_dist 1 "Sun 25 Jan 2004"
+.TH g_dist 1 "Mon 29 Aug 2005"
.SH NAME
g_dist
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_dist\fP
.BI "-f" " traj.xtc "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
+.BI "-[no]xvgr" ""
.BI "-dist" " real "
.SH DESCRIPTION
g_dist can calculate the distance between the centers of mass of two
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.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 "Sun 25 Jan 2004"
+.TH g_dyndom 1 "Mon 29 Aug 2005"
.SH NAME
g_dyndom
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_dyndom\fP
.BI "-f" " dyndom.pdb "
-.TH g_enemat 1 "Sun 25 Jan 2004"
+.TH g_enemat 1 "Mon 29 Aug 2005"
.SH NAME
g_enemat
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_enemat\fP
.BI "-f" " ener.edr "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]sum" ""
.BI "-skip" " int "
.BI "-[no]mean" ""
.BI "-[no]coulr" ""
.BI "-[no]coul14" ""
.BI "-[no]lj" ""
+.BI "-[no]lj" ""
.BI "-[no]lj14" ""
-.BI "-[no]bham" ""
+.BI "-[no]bhamsr" ""
+.BI "-[no]bhamlr" ""
.BI "-[no]free" ""
.BI "-temp" " real "
.SH DESCRIPTION
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]sum" " no"
Sum the energy terms selected rather than display them all
.BI "-[no]lj" " yes"
extract Lennard-Jones SR energies
+.BI "-[no]lj" " no"
+ extract Lennard-Jones LR energies
+
.BI "-[no]lj14" " no"
extract Lennard-Jones 1-4 energies
-.BI "-[no]bham" " no"
- extract Buckingham energies
+.BI "-[no]bhamsr" " no"
+ extract Buckingham SR energies
+
+.BI "-[no]bhamlr" " no"
+ extract Buckingham LR energies
.BI "-[no]free" " yes"
calculate free energy
-.TH g_energy 1 "Sun 25 Jan 2004"
+.TH g_energy 1 "Mon 29 Aug 2005"
.SH NAME
g_energy
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_energy\fP
.BI "-f" " ener.edr "
.BI "-oda" " orideva.xvg "
.BI "-odr" " oridevr.xvg "
.BI "-odt" " oridevt.xvg "
+.BI "-oten" " oriten.xvg "
.BI "-corr" " enecorr.xvg "
.BI "-vis" " visco.xvg "
.BI "-ravg" " runavgdf.xvg "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]fee" ""
.BI "-fetemp" " real "
.BI "-zero" " real "
.BI "-ndf" " int "
.BI "-[no]fluc" ""
.BI "-[no]orinst" ""
+.BI "-[no]ovec" ""
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.BI "-P" " enum "
the time and ensemble averages.
+Option
+.B -oten
+plots the eigenvalues of the molecular order
+tensor for each orientation restraint experiment. With option
+
+.B -ovec
+also the eigenvectors are plotted.
+
+
With
.B -fee
an estimate is calculated for the free-energy
.B Output, Opt.
xvgr/xmgr file
+.BI "-oten" " oriten.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-corr" " enecorr.xvg"
.B Output, Opt.
xvgr/xmgr file
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]fee" " no"
Do a free energy estimate
.BI "-[no]orinst" " no"
Analyse instantaneous orientation data
+.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
-.TH g_filter 1 "Sun 25 Jan 2004"
+.TH g_filter 1 "Mon 29 Aug 2005"
.SH NAME
g_filter
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_filter\fP
.BI "-f" " traj.xtc "
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
-.TH g_gyrate 1 "Sun 25 Jan 2004"
+.TH g_gyrate 1 "Mon 29 Aug 2005"
.SH NAME
g_gyrate
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_gyrate\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
.BI "-o" " gyrate.xvg "
.BI "-acf" " moi-acf.xvg "
-.BI "-n" " index.ndx "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-nmol" " int "
.BI "-[no]q" ""
.BI "-[no]p" ""
.BI "-[no]moi" ""
.BI "-endfit" " real "
.SH DESCRIPTION
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.
+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.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.B Input
Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
.BI "-o" " gyrate.xvg"
.B Output
xvgr/xmgr file
.B Output, Opt.
xvgr/xmgr file
-.BI "-n" " index.ndx"
-.B Input, Opt.
- Index file
-
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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"
Use absolute value of the charge of an atom as weighting factor instead of mass
-.TH g_h2order 1 "Sun 25 Jan 2004"
+.TH g_h2order 1 "Mon 29 Aug 2005"
.SH NAME
g_h2order
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_h2order\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-d" " string "
.BI "-sl" " int "
.SH DESCRIPTION
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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.
-.TH g_hbond 1 "Sun 25 Jan 2004"
+.TH g_hbond 1 "Mon 29 Aug 2005"
.SH NAME
g_hbond
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_hbond\fP
.BI "-f" " traj.xtc "
.BI "-hx" " hbhelix.xvg "
.BI "-hbn" " hbond.ndx "
.BI "-hbm" " hbmap.xpm "
+.BI "-don" " donor.xvg "
.BI "-dan" " danum.xvg "
+.BI "-life" " hblife.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
+.BI "-[no]xvgr" ""
.BI "-[no]ins" ""
.BI "-a" " real "
.BI "-r" " real "
.BI "-[no]nitacc" ""
.BI "-[no]contact" ""
.BI "-shell" " real "
-.BI "-[no]dump" ""
+.BI "-fitstart" " real "
+.BI "-temp" " real "
+.BI "-dump" " int "
.BI "-max_hb" " real "
.BI "-[no]merge" ""
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.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
each timeframe. This is especially usefull when using
.B -shell
.
+
+
+
+Note: options
+.B -ac
+,
+.B -life
+,
+.B -hbn
+and
+.B -hbm
+
+require an amount of memory proportional to the total numbers of donors
+times the total number of acceptors in the selected group(s).
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.B Output, Opt.
X PixMap compatible matrix file
+.BI "-don" " donor.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-dan" " danum.xvg"
.B Output, Opt.
xvgr/xmgr file
+.BI "-life" " hblife.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]ins" " no"
Analyze solvent insertion
.BI "-shell" " real" " -1"
when 0, only calculate hydrogen bonds within nm shell around one particle
-.BI "-[no]dump" " no"
- Dump all hydrogen bond ACFs (maximum 1000) in a single xvg file for debugging
+.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 "-temp" " real" " 298.15"
+ Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming
+
+.BI "-dump" " int" " 0"
+ Dump the first N hydrogen bond ACFs in a single xvg file for debugging
.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"
- H-bonds between the same donor and accepter, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF.
+ 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"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
+
+.BI "-fitfn" " enum" " none"
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+,
+.B vac
+,
+.B exp5
+,
+.B exp7
+or
+.B exp9
+
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_helix 1 "Sun 25 Jan 2004"
+.TH g_helix 1 "Mon 29 Aug 2005"
.SH NAME
g_helix
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_helix\fP
.BI "-s" " topol.tpr "
.BI "-[no]q" ""
.BI "-[no]F" ""
.BI "-[no]db" ""
+.BI "-prop" " enum "
.BI "-[no]ev" ""
.BI "-ahxstart" " int "
.BI "-ahxend" " int "
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
.BI "-[no]db" " no"
Print debug info
+.BI "-prop" " enum" " RAD"
+ Select property to weight eigenvectors with. WARNING experimental stuff:
+.B RAD
+,
+.B TWIST
+,
+.B RISE
+,
+.B LEN
+,
+.B NHX
+,
+.B DIP
+,
+.B RMS
+,
+.B CPHI
+,
+.B RMSA
+,
+.B PHI
+,
+.B PSI
+,
+.B HB3
+,
+.B HB4
+,
+.B HB5
+or
+.B CD222
+
+
.BI "-[no]ev" " no"
Write a new 'trajectory' file for ED
-.TH g_lie 1 "Sun 25 Jan 2004"
+.TH g_lie 1 "Mon 29 Aug 2005"
.SH NAME
g_lie
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_lie\fP
.BI "-f" " ener.edr "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-Elj" " real "
.BI "-Eqq" " real "
.BI "-Clj" " real "
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-Elj" " real" " 0"
Lennard-Jones interaction between ligand and solvent
-.TH g_mdmat 1 "Sun 25 Jan 2004"
+.TH g_mdmat 1 "Mon 29 Aug 2005"
.SH NAME
g_mdmat
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_mdmat\fP
.BI "-f" " traj.xtc "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
+.BI "-[no]xvgr" ""
.BI "-t" " real "
.BI "-nlevels" " int "
.SH DESCRIPTION
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-t" " real" " 1.5"
trunc distance
-.TH g_mindist 1 "Sun 25 Jan 2004"
+.TH g_mindist 1 "Mon 29 Aug 2005"
.SH NAME
g_mindist
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_mindist\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]matrix" ""
.BI "-[no]max" ""
.BI "-d" " real "
.BI "-[no]pi" ""
.BI "-[no]split" ""
+.BI "-ng" " int "
.SH DESCRIPTION
g_mindist computes the distance between one group and a number of
-other groups.
-Both the minimum distance and the number of contacts within a given
+other groups. Both the minimum distance
+(between any pair of atoms from the respective groups)
+and the number of contacts within a given
distance are written to two separate output files.
With
.B -or
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]matrix" " no"
Calculate half a matrix of group-group distances
.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
+
-.TH g_morph 1 "Sun 25 Jan 2004"
+.TH g_morph 1 "Mon 29 Aug 2005"
.SH NAME
g_morph
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_morph\fP
.BI "-f1" " conf1.gro "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-ninterm" " int "
.BI "-first" " real "
.BI "-last" " real "
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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
-.TH g_msd 1 "Sun 25 Jan 2004"
+.TH g_msd 1 "Mon 29 Aug 2005"
.SH NAME
g_msd
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_msd\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-type" " enum "
.BI "-lateral" " enum "
.BI "-ngroup" " int "
g_msd computes the mean square displacement (MSD) of atoms from
their initial positions. This provides an easy way to compute
the diffusion constant using the Einstein relation.
+The time between additional starting points for the MSD calculation
+is set with
+.B -trestart
+.
The diffusion constant is calculated by least squares fitting a
straight line through the MSD from
.B -beginfit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-type" " enum" " no"
Compute diffusion coefficient in one direction:
.B no
.BI "-[no]mw" " yes"
Mass weighted MSD
-.BI "-trestart" " time" " 0"
+.BI "-trestart" " time" " 10"
Time between restarting points in trajectory (ps)
-.BI "-beginfit" " time" " 0"
- Start time for fitting the MSD (ps)
+.BI "-beginfit" " time" " -1"
+ Start time for fitting the MSD (ps), -1 is 10%
.BI "-endfit" " time" " -1"
- End time for fitting the MSD (ps), -1 is till end
+ End time for fitting the MSD (ps), -1 is 90%
-.TH g_nmeig 1 "Sun 25 Jan 2004"
+.TH g_nmeig 1 "Mon 29 Aug 2005"
.SH NAME
g_nmeig
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_nmeig\fP
.BI "-f" " hessian.mtx "
.BI "-s" " topol.tpr "
-.BI "-o" " eigenval.xvg "
+.BI "-of" " eigenfreq.xvg "
+.BI "-ol" " eigenval.xvg "
.BI "-v" " eigenvec.trr "
.BI "-[no]h" ""
.BI "-nice" " int "
+.BI "-[no]xvgr" ""
.BI "-[no]m" ""
.BI "-first" " int "
.BI "-last" " int "
An ensemble of structures can be generated from the eigenvectors with
.B g_nmens
-.
+. When mass weighting is used, the generated eigenvectors
+will be scaled back to plain cartesian coordinates before generating the
+output - in this case they will no longer be exactly orthogonal in the
+standard cartesian norm (But in the mass weighted norm they would be).
.SH FILES
.BI "-f" " hessian.mtx"
.B Input
.B Input
Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-.BI "-o" " eigenval.xvg"
+.BI "-of" " eigenfreq.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-ol" " eigenval.xvg"
.B Output
xvgr/xmgr file
.BI "-nice" " int" " 19"
Set the nicelevel
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.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"
First eigenvector to write away
-.BI "-last" " int" " 100"
+.BI "-last" " int" " 50"
Last eigenvector to write away
-.TH g_nmens 1 "Sun 25 Jan 2004"
+.TH g_nmens 1 "Mon 29 Aug 2005"
.SH NAME
g_nmens
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_nmens\fP
.BI "-v" " eigenvec.trr "
.BI "-o" " ensemble.xtc "
.BI "-[no]h" ""
.BI "-nice" " int "
+.BI "-[no]xvgr" ""
.BI "-temp" " real "
.BI "-seed" " int "
.BI "-num" " int "
.BI "-nice" " int" " 19"
Set the nicelevel
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-temp" " real" " 300"
Temperature in Kelvin
-.TH g_order 1 "Sun 25 Jan 2004"
+.TH g_order 1 "Mon 29 Aug 2005"
.SH NAME
g_order
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_order\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-d" " enum "
.BI "-sl" " int "
.BI "-[no]szonly" ""
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-d" " enum" " z"
Direction of the normal on the membrane:
.B z
-.TH g_potential 1 "Sun 25 Jan 2004"
+.TH g_potential 1 "Mon 29 Aug 2005"
.SH NAME
g_potential
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_potential\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-d" " string "
.BI "-sl" " int "
.BI "-cb" " int "
.BI "-ce" " int "
.BI "-tz" " real "
.BI "-[no]spherical" ""
+.BI "-ng" " int "
.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 "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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 "-[no]spherical" " no"
Calculate spherical thingie
+.BI "-ng" " int" " 1"
+ Number of groups to consider
+
\- Discarding slices for integration should not be necessary.
-.TH g_rama 1 "Sun 25 Jan 2004"
+.TH g_rama 1 "Mon 29 Aug 2005"
.SH NAME
g_rama
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_rama\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.SH DESCRIPTION
g_rama selects the Phi/Psi dihedral combinations from your topology file
and computes these as a function of time.
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
-.TH g_rdf 1 "Sun 25 Jan 2004"
+.TH g_rdf 1 "Mon 29 Aug 2005"
.SH NAME
g_rdf
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_rdf\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-bin" " real "
.BI "-[no]com" ""
+.BI "-[no]pbc" ""
+.BI "-[no]xy" ""
.BI "-cut" " real "
+.BI "-ng" " int "
.BI "-fade" " real "
.BI "-nlevel" " int "
.BI "-startq" " real "
g_rdf calculates radial distribution functions in different ways.
The normal method is around a (set of) particle(s), the other method
is around the center of mass of a set of particles.
+With both methods rdf's can also be calculated around axes parallel
+to the z-axis with option
+.B -xy
+.
If a run input file is supplied (
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
-.BI "-bin" " real" " 0.001"
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-bin" " real" " 0.002"
Binwidth (nm)
.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 "-[no]xy" " no"
+ Use only the x and y components of the distance
+
.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"
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.
-.TH g_rms 1 "Sun 25 Jan 2004"
+.TH g_rms 1 "Mon 29 Aug 2005"
.SH NAME
g_rms
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_rms\fP
.BI "-s" " topol.tpr "
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-what" " enum "
.BI "-[no]pbc" ""
.BI "-fit" " enum "
.BI "-bmax" " real "
.BI "-bmin" " real "
.BI "-nlevels" " int "
+.BI "-ng" " int "
.SH DESCRIPTION
g_rms compares two structures by computing the root mean square
deviation (RMSD), the size-independent 'rho' similarity parameter
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-what" " enum" " rmsd"
Structural difference measure:
.B rmsd
.BI "-nlevels" " int" " 80"
Number of levels in the matrices
+.BI "-ng" " int" " 1"
+ Number of groups to compute RMS between
+
-.TH g_rmsdist 1 "Sun 25 Jan 2004"
+.TH g_rmsdist 1 "Mon 29 Aug 2005"
.SH NAME
g_rmsdist
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_rmsdist\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-nlevels" " int "
.BI "-max" " real "
.BI "-[no]sumh" ""
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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
-.TH g_rmsf 1 "Sun 25 Jan 2004"
+.TH g_rmsf 1 "Mon 29 Aug 2005"
.SH NAME
g_rmsf
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]res" ""
.BI "-[no]aniso" ""
.SH DESCRIPTION
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]res" " no"
Calculate averages for each residue
-.TH g_rotacf 1 "Sun 25 Jan 2004"
+.TH g_rotacf 1 "Mon 29 Aug 2005"
.SH NAME
g_rotacf
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_rotacf\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]d" ""
.BI "-[no]aver" ""
.BI "-acflen" " int "
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]d" " no"
Use index doublets (vectors) for correlation function instead of triplets (planes)
-.TH g_saltbr 1 "Sun 25 Jan 2004"
+.TH g_saltbr 1 "Mon 29 Aug 2005"
.SH NAME
g_saltbr
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_saltbr\fP
.BI "-f" " traj.xtc "
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-t" " real" " 1000"
-.TH g_sas 1 "Sun 25 Jan 2004"
+.TH g_sas 1 "Mon 29 Aug 2005"
.SH NAME
g_sas
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_sas\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-solsize" " real "
.BI "-ndots" " int "
.BI "-qmax" " real "
g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area.
As a side effect the Connolly surface can be generated as well in
a pdb file where the nodes are represented as atoms and the vertices
-connecting the nearest nodes as CONECT records. The area can be plotted
+connecting the nearest nodes as CONECT records.
+The program will ask for a group for the surface calculation
+and a group for the output. The calculation group should always
+consists of all the non-solvent atoms in the system.
+The output group can be the whole or part of the calculation group.
+The area can be plotted
per residue and atom as well (options
.B -or
and
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-solsize" " real" " 0.14"
Radius of the solvent probe (nm)
-.TH g_sgangle 1 "Sun 25 Jan 2004"
+.TH g_sgangle 1 "Mon 29 Aug 2005"
.SH NAME
g_sgangle
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_sgangle\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-[no]pbc" ""
+.BI "-[no]one" ""
+.BI "-[no]z" ""
.SH DESCRIPTION
Compute the angle and distance between two groups.
The groups are defined by a number of atoms given in an index file and
may be two or three atoms in size.
+If -one is set, only one group should be specified in the index
+file and the angle between this group at time 0 and t will be computed.
The angles calculated depend on the order in which the atoms are
given. Giving for instance 5 6 will rotate the vector 5-6 with
180 degrees compared to giving 6 5.
xvgr/xmgr file
.BI "-od" " sg_dist.xvg"
-.B Output
+.B Output, Opt.
xvgr/xmgr file
.BI "-od1" " sg_dist1.xvg"
-.B Output
+.B Output, Opt.
xvgr/xmgr file
.BI "-od2" " sg_dist2.xvg"
-.B Output
+.B Output, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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"
+ Only one group compute angle between vector at time zero and time t
+
+.BI "-[no]z" " no"
+ Use the Z-axis as reference
+
-.TH g_sorient 1 "Sun 25 Jan 2004"
+.TH g_sorient 1 "Mon 29 Aug 2005"
.SH NAME
g_sorient
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_sorient\fP
.BI "-f" " traj.xtc "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]com" ""
.BI "-rmin" " real "
.BI "-rmax" " real "
-.BI "-nbin" " int "
+.BI "-bin" " real "
.BI "-[no]pbc" ""
.SH DESCRIPTION
g_sorient analyzes solvent orientation around solutes.
.B -o
-: angle distribution of theta1.
+: distribtion of cos(theta1) for rmin=r=rmax.
.B -no
-: angle distribution of theta2.
+: distribution of 3cos2(theta2)-1 for rmin=r=rmax.
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]com" " no"
Use the center of mass as the reference postion
.BI "-rmax" " real" " 0.5"
Maximum distance
-.BI "-nbin" " int" " 20"
- Number of bins
+.BI "-bin" " real" " 0.02"
+ Binwidth
.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 "Sun 25 Jan 2004"
+.TH g_tcaf 1 "Mon 29 Aug 2005"
.SH NAME
g_tcaf
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_tcaf\fP
.BI "-f" " traj.trr "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]mol" ""
.BI "-[no]k34" ""
.BI "-wt" " real "
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
.SH DESCRIPTION
g_tcaf computes tranverse current autocorrelations.
These are used to estimate the shear viscosity eta.
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]mol" " no"
Calculate tcaf of molecules
.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"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
+
+.BI "-fitfn" " enum" " none"
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+,
+.B vac
+,
+.B exp5
+,
+.B exp7
+or
+.B exp9
+
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
-.TH g_traj 1 "Sun 25 Jan 2004"
+.TH g_traj 1 "Mon 29 Aug 2005"
.SH NAME
g_traj
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_traj\fP
.BI "-f" " traj.xtc "
.BI "-ot" " temp.xvg "
.BI "-ekt" " ektrans.xvg "
.BI "-ekr" " ekrot.xvg "
+.BI "-vd" " veldist.xvg "
.BI "-cv" " veloc.pdb "
.BI "-cf" " force.pdb "
.BI "-[no]h" ""
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]com" ""
.BI "-[no]mol" ""
.BI "-[no]nojump" ""
.BI "-[no]x" ""
.BI "-[no]y" ""
.BI "-[no]z" ""
+.BI "-ng" " int "
.BI "-[no]len" ""
+.BI "-bin" " real "
.BI "-scale" " real "
.SH DESCRIPTION
g_traj plots coordinates, velocities, forces and/or the box.
the
.B -nojump
option to obtain the correct average coordinates.
+
+
+Option
+.B -vd
+computes a velocity distribution, i.e. the
+norm of the vector is plotted. In addition in the same graph
+the kinetic energy distribution is given.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.B Output, Opt.
xvgr/xmgr file
+.BI "-vd" " veldist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-cv" " veloc.pdb"
.B Output, Opt.
Protein data bank file
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-[no]com" " no"
Plot data for the com of each group
.BI "-[no]z" " yes"
Plot Z-component
+.BI "-ng" " int" " 1"
+ Number of groups to consider
+
.BI "-[no]len" " no"
Plot vector length
+.BI "-bin" " real" " 1"
+ Binwidth for velocity histogram (nm/ps)
+
.BI "-scale" " real" " 0"
Scale factor for pdb output, 0 is autoscale
-.TH g_velacc 1 "Sun 25 Jan 2004"
+.TH g_velacc 1 "Mon 29 Aug 2005"
.SH NAME
g_velacc
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_velacc\fP
.BI "-f" " traj.trr "
.BI "-e" " time "
.BI "-dt" " time "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-[no]mol" ""
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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
-.TH g_wham 1 "Sun 25 Jan 2004"
+.TH g_wham 1 "Mon 29 Aug 2005"
.SH NAME
g_wham
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3g_wham\fP
.BI "-o" " profile.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-min" " real "
.BI "-max" " real "
.BI "-bins" " int "
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-min" " real" " 0"
Minimum coordinate in profile
-.TH genbox 1 "Sun 25 Jan 2004"
+.TH genbox 1 "Mon 29 Aug 2005"
.SH NAME
genbox
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3genbox\fP
.BI "-cp" " protein.gro "
-.TH genconf 1 "Sun 25 Jan 2004"
+.TH genconf 1 "Mon 29 Aug 2005"
.SH NAME
genconf
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3genconf\fP
.BI "-f" " conf.gro "
.BI "-maxrot" " vector" " 90 90 90"
Maximum random rotation
-.BI "-[no]renumber" " no"
+.BI "-[no]renumber" " yes"
Renumber residues
\- The program should allow for random displacement off lattice points.
-.TH genion 1 "Sun 25 Jan 2004"
+.TH genion 1 "Mon 29 Aug 2005"
.SH NAME
genion
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3genion\fP
.BI "-s" " topol.tpr "
.BI "-pot" " pot.pdb "
.BI "-[no]h" ""
.BI "-nice" " int "
+.BI "-[no]xvgr" ""
.BI "-np" " int "
.BI "-pname" " string "
.BI "-pq" " real "
.BI "-nice" " int" " 19"
Set the nicelevel
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-np" " int" " 0"
Number of positive ions
-.TH genpr 1 "Sun 25 Jan 2004"
+.TH genpr 1 "Mon 29 Aug 2005"
.SH NAME
genpr
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3genpr\fP
.BI "-f" " conf.gro "
-.TH gmxcheck 1 "Sun 25 Jan 2004"
+.TH gmxcheck 1 "Mon 29 Aug 2005"
.SH NAME
gmxcheck
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3gmxcheck\fP
.BI "-f" " traj.xtc "
.BI "-c" " topol.tpr "
.BI "-e" " ener.edr "
.BI "-e2" " ener2.edr "
+.BI "-n" " index.ndx "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-vdwfac" " real "
will be calculated from them.
-The program will compare run input (
+If an index file is given it's contents will be sumamrized.
+
+
+If both a trajectory and a tpr file are given (with
+.B -s1
+)
+the program will check whether the bond lengths defined in the tpr
+file are indeed correct in the trajectory. If not you may have
+non-matching files due to e.g. deshuffling or due to problems with
+virtual sites. With these flags, gmxcheck provides a quick check for such problems.
+
+The program can compare run two input (
.B .tpr
,
.B .tpb
.B Input, Opt.
Generic energy: edr ene
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-bonhi" " real" " 0.7"
Max. fract. of sum of VdW radii for bonded atoms
-.BI "-tol" " real" " 0"
+.BI "-tol" " real" " 0.001"
Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)
.BI "-lastener" " string" " "
-.TH gmxdump 1 "Sun 25 Jan 2004"
+.TH gmxdump 1 "Mon 29 Aug 2005"
.SH NAME
gmxdump
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3gmxdump\fP
.BI "-s" " topol.tpr "
-.TH grompp 1 "Sun 25 Jan 2004"
+.TH grompp 1 "Mon 29 Aug 2005"
.SH NAME
grompp
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3grompp\fP
.BI "-f" " grompp.mdp "
.BI "-np" " int "
.BI "-[no]shuffle" ""
.BI "-[no]sort" ""
-.BI "-[no]rmdumbds" ""
+.BI "-[no]rmvsbds" ""
.BI "-load" " string "
.BI "-maxwarn" " int "
.BI "-[no]check14" ""
.B -e
to have exact restarts when using pressure and/or
-temperature coupling. For an exact restart do not forget to turn off
-velocity generation and turn on unconstrained starting when constraints
-are present in the system.
+Nose-Hoover temperature coupling. For an exact restart do not forget
+to turn off velocity generation and turn on unconstrained starting
+when constraints are present in the system.
If you want to continue a crashed run, it is
easier to use
.B tpbconv
By default all bonded interactions which have constant energy due to
-dummy atom constructions will be removed. If this constant energy is
+virtual site constructions will be removed. If this constant energy is
not zero, this will result in a shift in the total energy. All bonded
interactions can be kept by turning off
-.B -rmdumbds
+.B -rmvsbds
. Additionally,
all constraints for distances which will be constant anyway because
-of dummy atom constructions will be removed. If any constraints remain
-which involve dummy atoms, a fatal error will result.
+of virtual site constructions will be removed. If any constraints remain
+which involve virtual sites, a fatal error will result.
To verify your run input file, please make notice of all warnings
on the screen, and correct where necessary. Do also look at the contents
.BI "-[no]sort" " no"
Sort molecules according to X coordinate
-.BI "-[no]rmdumbds" " yes"
- Remove constant bonded interactions with dummies
+.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
-.TH highway 1 "Sun 25 Jan 2004"
+.TH highway 1 "Mon 29 Aug 2005"
.SH NAME
highway
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3highway\fP
.BI "-f" " highway.dat "
-.BI "-a" " auto.dat "
.BI "-[no]h" ""
.BI "-nice" " int "
-.BI "-b" " time "
-.BI "-e" " time "
-.BI "-dt" " time "
.SH DESCRIPTION
highway is the gromacs highway simulator. It is an X-windows
-gadget that shows a (periodic) autobahn with a user defined
+gadget that shows a (periodic) Autobahn with a user defined
number of cars. Fog can be turned on or off to increase the
-number of crashes. Nice for a background CPU-eater
+number of crashes. Nice for a background CPU-eater. A sample
+input file is in $GMXDATA/top/highway.dat
.SH FILES
.BI "-f" " highway.dat"
.B Input
Generic data file
-.BI "-a" " auto.dat"
-.B Input
- Generic data file
-
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " -1"
- First frame (ps) to read from trajectory
-
-.BI "-e" " time" " -1"
- Last frame (ps) to read from trajectory
-
-.BI "-dt" " time" " -1"
- Only use frame when t MOD dt = first time (ps)
-
-.TH make_ndx 1 "Sun 25 Jan 2004"
+.TH make_ndx 1 "Mon 29 Aug 2005"
.SH NAME
make_ndx
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3make_ndx\fP
.BI "-f" " conf.gro "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-natoms" " int "
-.BI "-[no]verbose" ""
.SH DESCRIPTION
Index groups are necessary for almost every gromacs program.
All these programs can generate default index groups. You ONLY
.BI "-natoms" " int" " 0"
set number of atoms (default: read from coordinate or index file)
-.BI "-[no]verbose" " no"
- Verbose output
-
-.TH mdrun 1 "Sun 25 Jan 2004"
+.TH mdrun 1 "Mon 29 Aug 2005"
.SH NAME
mdrun
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3mdrun\fP
.BI "-s" " topol.tpr "
.BI "-dgdl" " dgdl.xvg "
.BI "-field" " field.xvg "
.BI "-table" " table.xvg "
+.BI "-tablep" " tablep.xvg "
.BI "-rerun" " rerun.xtc "
+.BI "-tpi" " tpi.xvg "
.BI "-ei" " sam.edi "
.BI "-eo" " sam.edo "
.BI "-j" " wham.gct "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-deffnm" " string "
+.BI "-[no]xvgr" ""
.BI "-np" " int "
.BI "-nt" " int "
.BI "-[no]v" ""
.BI "-[no]compact" ""
+.BI "-[no]sepdvdl" ""
.BI "-[no]multi" ""
+.BI "-replex" " int "
+.BI "-reseed" " int "
.BI "-[no]glas" ""
.BI "-[no]ionize" ""
.SH DESCRIPTION
eigenvectors.
-The -table option can be used to pass mdrun a formatted table with
-user-defined 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, for 6-8, 6-9, 6-10, 6-11, 6-12
-Lennard Jones potentials with normal Coulomb.
+When user-defined potential functions have been selected in the
+
+.B .mdp
+file the
+.B -table
+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,
+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
+functions is read using the
+.B -tablep
+option.
The options
See manual.
+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,
+for instance topol.tpr becomes topol0.tpr, topol1.tpr etc.
+The main 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
+.B -multi
+, 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
+
+.B -reseed
+. The velocities are scaled and neighbor searching
+is performed after every exchange.
+
+
Finally some experimental algorithms can be tested when the
appropriate options have been given. Currently under
-investigation are: polarizibility, glass simulations,
-Free energy perturbation, X-Ray bombardments
-and parallel independent simulations.
+investigation are: polarizibility, glass simulations
+and X-Ray bombardments.
When mdrun receives a TERM signal, it will set nsteps to the current
.B Input, Opt.
xvgr/xmgr file
+.BI "-tablep" " tablep.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
.BI "-rerun" " rerun.xtc"
.B Input, Opt.
Generic trajectory: xtc trr trj gro g96 pdb
+.BI "-tpi" " tpi.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-ei" " sam.edi"
.B Input, Opt.
ED sampling input
General coupling stuff
.BI "-jo" " bam.gct"
-.B Input, Opt.
+.B Output, Opt.
General coupling stuff
.BI "-ffout" " gct.xvg"
.BI "-deffnm" " string" " "
Set the default filename for all file options
+.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]compact" " yes"
Write a compact log file
+.BI "-[no]sepdvdl" " 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 "-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"
Do glass simulation with special long range corrections
-.TH mk_angndx 1 "Sun 25 Jan 2004"
+.TH mk_angndx 1 "Mon 29 Aug 2005"
.SH NAME
mk_angndx
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3mk_angndx\fP
.BI "-s" " topol.tpr "
-.TH ngmx 1 "Sun 25 Jan 2004"
+.TH ngmx 1 "Mon 29 Aug 2005"
.SH NAME
ngmx
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3ngmx\fP
.BI "-f" " traj.xtc "
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
\- Balls option does not work
-.TH pdb2gmx 1 "Sun 25 Jan 2004"
+.TH pdb2gmx 1 "Mon 29 Aug 2005"
.SH NAME
pdb2gmx
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3pdb2gmx\fP
.BI "-f" " eiwit.pdb "
.BI "-[no]una" ""
.BI "-[no]ignh" ""
.BI "-[no]missing" ""
+.BI "-[no]v" ""
.BI "-posrefc" " real "
-.BI "-dummy" " enum "
+.BI "-vsite" " enum "
.BI "-[no]heavyh" ""
.BI "-[no]deuterate" ""
.SH DESCRIPTION
-The force fields supported currently are:
+The force fields in the distribution are currently:
-G43a1 GROMOS96 43a1 Forcefield (official distribution)
+oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
+G43b1 GROMOS96 43b1 Vacuum Forcefield
-oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
+G43a1 GROMOS96 43a1 Forcefield
+G43a2 GROMOS96 43a2 Forcefield (improved alkane dihedrals)
-G43b1 GROMOS96 43b1 Vacuum Forcefield (official distribution)
+G45a3 GROMOS96 45a3 Forcefield
+G53a5 GROMOS96 53a5 Forcefield
+
+G53a6 GROMOS96 53a6 Forcefield
gmx Gromacs Forcefield (a modified GROMOS87, see manual)
+encads Encad all-atom force field, using scaled-down vacuum charges
-G43a2 GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
+encadv Encad all-atom force field, using full solvent charges
The corresponding data files can be found in the library directory
with names like ffXXXX.YYY. Check chapter 5 of the manual for more
-information about file formats.
+information about file formats. By default the forcefield selection
+is interactive, but you can use the
+.B -ff
+option to specify
+one of the short names above on the command line instead. In that
+case pdb2gmx just looks for the corresponding file.
Note that a pdb file is nothing more than a file format, and it
Option
.B -merge
will ask if you want to merge consecutive chains
-into one molecule, this can be useful for connecting chains with a
-disulfide brigde.
+into one molecule definition, this can be useful for connecting chains
+with a disulfide brigde or intermolecular distance restraints.
pdb2gmx will also check the occupancy field of the pdb file.
The option
-.B -dummy
+.B -vsite
removes hydrogen and fast improper dihedral
motions. Angular and out-of-plane motions can be removed by changing
-hydrogens into dummy atoms and fixing angles, which fixes their
+hydrogens into virtual sites and fixing angles, which fixes their
position relative to neighboring atoms. Additionally, all atoms in the
aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)
-can be converted into dummy atoms, elminating the fast improper dihedral
+can be converted into virtual sites, elminating the fast improper dihedral
fluctuations in these rings. Note that in this case all other hydrogen
-atoms are also converted to dummy atoms. The mass of all atoms that are
-converted into dummy atoms, is added to the heavy atoms.
+atoms are also converted to virtual sites. The mass of all atoms that are
+converted into virtual sites, is added to the heavy atoms.
Also slowing down of dihedral motion can be done with
Set the nicelevel
.BI "-[no]merge" " no"
- Merge multiple chains into one molecule
+ Merge chains into one molecule definition
-.BI "-ff" " string" " G43a1"
- Select the force field, supported are: G43a1, oplsaa, gmx, G43a2, G43b1. Run pdb2gmx -h for more information.
+.BI "-ff" " string" " select"
+ Force field, interactive by default. Use -h for information.
.BI "-water" " enum" " spc"
Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P:
.B tip3p
,
.B tip4p
-or
+,
.B tip5p
+or
+.B f3c
.BI "-[no]inter" " no"
.BI "-[no]missing" " no"
Continue when atoms are missing, dangerous
+.BI "-[no]v" " no"
+ Be slightly more verbose in messages
+
.BI "-posrefc" " real" " 1000"
Force constant for position restraints
-.BI "-dummy" " enum" " none"
- Convert atoms to dummy atoms:
+.BI "-vsite" " enum" " none"
+ Convert atoms to virtual sites:
.B none
,
.B hydrogens
-.TH protonate 1 "Sun 25 Jan 2004"
+.TH protonate 1 "Mon 29 Aug 2005"
.SH NAME
protonate
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3protonate\fP
.BI "-s" " topol.tpr "
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
-.TH tpbconv 1 "Sun 25 Jan 2004"
+.TH tpbconv 1 "Mon 29 Aug 2005"
.SH NAME
tpbconv
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3tpbconv\fP
.BI "-s" " topol.tpr "
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.
-When pressure and/or temperature coupling is used an energy file
-can be supplied to get an exact continuation of the original run.
+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.
-.TH trjcat 1 "Sun 25 Jan 2004"
+.TH trjcat 1 "Mon 29 Aug 2005"
.SH NAME
trjcat
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3trjcat\fP
.BI "-f" " traj.xtc "
.BI "-o" " trajout.xtc "
.BI "-n" " index.ndx "
+.BI "-demux" " remd.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-tu" " enum "
+.BI "-[no]xvgr" ""
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
which implies you do not need to store double the amount of data.
Obviously the file to append to has to be the one with lowest starting
time since one can only append at the end of a file.
+
+
+If the
+.B -demux
+option is given, the N trajectories that are
+read, are written in another order as specified in the xvg file.The xvg file should contain something like:
+
+
+0 0 1 2 3 4 5
+
+2 1 0 2 3 5 4
+
+Where the first number is the time, and subsequent numbers point to
+trajectory indices.
+The frames corresponding to the numbers present at the first line
+are collected into the output trajectory. If the number of frames in
+the trajectory does not match that in the xvg file then the program
+tries to be smart. Beware.
.SH FILES
.BI "-f" " traj.xtc"
.B Input, Mult.
Generic trajectory: xtc trr trj gro g96 pdb
.BI "-o" " trajout.xtc"
-.B Output
+.B Output, Mult.
Generic trajectory: xtc trr trj gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
+.BI "-demux" " remd.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.B h
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-b" " time" " -1"
First time to use (ps)
-.TH trjconv 1 "Sun 25 Jan 2004"
+.TH trjconv 1 "Mon 29 Aug 2005"
.SH NAME
trjconv
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3trjconv\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-fr" " frames.ndx "
+.BI "-sub" " cluster.ndx "
+.BI "-drop" " drop.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
.BI "-skip" " int "
.BI "-dt" " time "
.BI "-dump" " time "
.BI "-timestep" " time "
.BI "-pbc" " enum "
.BI "-ur" " enum "
-.BI "-[no]center" ""
+.BI "-center" " enum "
.BI "-box" " vector "
.BI "-shift" " vector "
.BI "-fit" " enum "
.BI "-split" " time "
.BI "-[no]sep" ""
.BI "-[no]ter" ""
+.BI "-dropunder" " real "
+.BI "-dropover" " real "
.SH DESCRIPTION
trjconv can convert trajectory files in many ways:
.B 2.
select a subset of atoms
-
.B 3.
remove periodicity from molecules
)
+.B 9.
+cut the trajectory in small subtrajectories according
+to information in an index file. This allows subsequent analysis of
+the subtrajectories that could, for example be the result of a
+cluster analysis. Use option
+.B -sub
+.
+This assumes that the entries in the index file are frame numbers and
+dumps each group in the index file to a separate trajectory file.
+
+
+.B 10.
+select frames within a certain range of a quantity given
+in an
+.B .xvg
+file.
+
The program
.B trjcat
.B compact
puts all atoms at the closest distance from the center
of the box. This can be useful for visualizing e.g. truncated
-octahedrons.
+octahedrons. The center for options
+.B tric
+and
+.B compact
+
+is
+.B tric
+(see below), unless the option
+.B -center
+
+is set differently.
Option
.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:
+
+.B tric
+: half of the sum of the box vectors,
+
+.B rect
+: half of the box diagonal,
+
+.B zero
+: zero.
Use option
.B -pbc whole
in addition to
.B -dump
can be used to extract a frame at or near
one specific time from your trajectory.
+
+
+Option
+.B -drop
+reads an
+.B .xvg
+file with times and values.
+When options
+.B -dropunder
+and/or
+.B -dropover
+are set,
+frames with a value below and above the value of the respective options
+will not be written.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.B Input, Opt.
Index file
+.BI "-sub" " cluster.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-drop" " drop.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
.BI "-tu" " enum" " ps"
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
+.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
.B compact
-.BI "-[no]center" " no"
- Center atoms in box
+.BI "-center" " enum" " no"
+ Center atoms in box:
+.B no
+,
+.B tric
+,
+.B rect
+or
+.B zero
+
.BI "-box" " vector" " 0 0 0"
Size for new cubic box (default: read from input)
.BI "-[no]ter" " no"
Use 'TER' in pdb file as end of frame in stead of default 'ENDMDL'
+.BI "-dropunder" " real" " 0"
+ Drop all frames below this value
+
+.BI "-dropover" " real" " 0"
+ Drop all frames above this value
+
-.TH trjorder 1 "Sun 25 Jan 2004"
+.TH trjorder 1 "Mon 29 Aug 2005"
.SH NAME
trjorder
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3trjorder\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-o" " ordered.xtc "
+.BI "-nshell" " nshell.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
+.BI "-[no]xvgr" ""
.BI "-na" " int "
.BI "-da" " int "
+.BI "-[no]com" ""
+.BI "-r" " real "
.SH DESCRIPTION
trjorder orders molecules according to the smallest distance
to atoms in a reference group. It will ask for a group of reference
.B Output
Generic trajectory: xtc trr trj gro g96 pdb
+.BI "-nshell" " nshell.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
.BI "-na" " int" " 3"
Number of atoms in a molecule
.BI "-da" " int" " 1"
Atom used for the distance calculation
+.BI "-[no]com" " no"
+ Use the distance to the center of mass of the reference group
+
+.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 "Sun 25 Jan 2004"
+.TH wheel 1 "Mon 29 Aug 2005"
.SH NAME
wheel
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3wheel\fP
.BI "-f" " nnnice.dat "
-.TH x2top 1 "Sun 25 Jan 2004"
+.TH x2top 1 "Mon 29 Aug 2005"
.SH NAME
x2top
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3x2top\fP
.BI "-f" " conf.gro "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-scale" " real "
-.BI "-ff" " enum "
+.BI "-ff" " string "
.BI "-nexcl" " int "
.BI "-[no]H14" ""
.BI "-[no]alldih" ""
and force constants will be printed in the topology for all
interactions. The equilibrium distances and angles are taken
from the input coordinates, the force constant are set with
-command line options.
+command line options.The force fields supported currently are:
+
+
+G43a1 GROMOS96 43a1 Forcefield (official distribution)
+
+
+oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
+
+
+G43b1 GROMOS96 43b1 Vacuum Forcefield (official distribution)
+
+
+gmx Gromacs Forcefield (a modified GROMOS87, see manual)
+
+
+G43a2 GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
+
+
+The corresponding data files can be found in the library directory
+with names like ffXXXX.YYY. Check chapter 5 of the manual for more
+information about file formats. By default the forcefield selection
+is interactive, but you can use the
+.B -ff
+option to specify
+one of the short names above on the command line instead. In that
+case pdb2gmx just looks for the corresponding file.
+
+
.SH FILES
.BI "-f" " conf.gro"
.B Input
.BI "-scale" " real" " 1.1"
Scaling factor for bonds with unknown atom types relative to atom type O
-.BI "-ff" " enum" " G43a1"
- Select the force field for your simulation:
-.B G43a1
-,
-.B oplsaa
-,
-.B gmx
-,
-.B G43a2
-or
-.B G43b1
-
+.BI "-ff" " string" " select"
+ Select the force field for your simulation.
.BI "-nexcl" " int" " 3"
Number of exclusions
-.TH xpm2ps 1 "Sun 25 Jan 2004"
+.TH xpm2ps 1 "Mon 29 Aug 2005"
.SH NAME
xpm2ps
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3xpm2ps\fP
.BI "-f" " root.xpm "
.BI "-legend" " enum "
.BI "-diag" " enum "
.BI "-combine" " enum "
+.BI "-size" " real "
.BI "-bx" " real "
.BI "-by" " real "
.BI "-rainbow" " enum "
sets yfont, ytickfont and xtickfont.
+When no
+.B m2p
+file is supplied, many setting are set by
+command line options. The most important option is
+.B -size
+
+which sets the size of the whole matrix in postscript units.
+This option can be overridden with the
+.B -bx
+and
+.B -by
+
+options (and the corresponding parameters in the
+.B m2p
+file),
+which set the size of a single matrix element.
+
+
With
.B -f2
a 2nd matrix file can be supplied, both matrix
.B div
+.BI "-size" " real" " 400"
+ Horizontal size of the matrix in ps units
+
.BI "-bx" " real" " 0"
- Box x-size (also y-size when -by is not set)
+ Element x-size, overrides -size (also y-size when -by is not set)
.BI "-by" " real" " 0"
- Box y-size
+ Element y-size
.BI "-rainbow" " enum" " no"
Rainbow colors, convert white to:
-.TH xrama 1 "Sun 25 Jan 2004"
+.TH xrama 1 "Mon 29 Aug 2005"
.SH NAME
xrama
-.B VERSION 3.2.0
+.B VERSION 3.3_beta_20050823
.SH SYNOPSIS
\f3xrama\fP
.BI "-f" " traj.xtc "
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " -1"
+.BI "-b" " time" " 0"
First frame (ps) to read from trajectory
-.BI "-e" " time" " -1"
+.BI "-e" " time" " 0"
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " -1"
+.BI "-dt" " time" " 0"
Only use frame when t MOD dt = first time (ps)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff