NAME
gmxcheck - checks and compares files
VERSION 4.0.1
SYNOPSIS
gmxcheck -f traj.xtc -f2 traj.xtc -s1 top1.tpr -s2 top2.tpr -c
topol.tpr -e ener.edr -e2 ener2.edr -n index.ndx -m doc.tex -[no]h
-nice int -vdwfac real -bonlo real -bonhi real -tol real -[no]ab
-lastener string
DESCRIPTION
gmxcheck reads a trajectory ( .trj, .trr or .xtc), an energy file (
.ene or .edr) or an index file ( .ndx) and prints out useful
information about them.
Option -c checks for presence of coordinates, velocities and box in
the file, for close contacts (smaller than -vdwfac and not bonded,
i.e. not between -bonlo and -bonhi, all relative to the sum of both
Van der Waals radii) and atoms outside the box (these may occur often
and are no problem). If velocities are present, an estimated
temperature will be calculated from them.
If an index file is given it’s contents will be sumamrized.
If both a trajectory and a tpr file are given (with -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 ( .tpr, .tpb or .tpa) files
when both -s1 and -s2 are supplied. Similarly a pair of trajectory
files can be compared (using the -f2 option), or a pair of energy
files (using the -e2 option).
For free energy simulations the A and B state topology from one run
input file can be compared with options -s1 and -ab.
In case the -m flag is given a LaTeX file will be written consisting a
rough outline for a methods section for a paper.
FILES
-f traj.xtc Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-f2 traj.xtc Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-s1 top1.tpr Input, Opt.
Run input file: tpr tpb tpa
-s2 top2.tpr Input, Opt.
Run input file: tpr tpb tpa
-c topol.tpr Input, Opt.
Structure+mass(db): tpr tpb tpa gro g96 pdb
-e ener.edr Input, Opt.
Energy file: edr ene
-e2 ener2.edr Input, Opt.
Energy file: edr ene
-n index.ndx Input, Opt.
Index file
-m doc.tex Output, Opt.
LaTeX file
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 0
Set the nicelevel
-vdwfac real 0.8
Fraction of sum of VdW radii used as warning cutoff
-bonlo real 0.4
Min. fract. of sum of VdW radii for bonded atoms
-bonhi real 0.7
Max. fract. of sum of VdW radii for bonded atoms
-tol real 0.001
Relative tolerance for comparing real values defined as
2*(a-b)/(|a|+|b|)
-[no]abno
Compare the A and B topology from one file
-lastener string
Last energy term to compare (if not given all are tested). It makes
sense to go up until the Pressure.
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 gmxcheck(1)