gmx-check(1) GROMACS Manual gmx-check(1)NAMEgmx-check - Check and compare files
SYNOPSIS
gmx check [-f [<.xtc/.trr/...>]] [-f2 [<.xtc/.trr/...>]]
[-s1 [<.tpr/.tpb/...>]] [-s2 [<.tpr/.tpb/...>]]
[-c [<.tpr/.tpb/...>]] [-e [<.edr>]] [-e2 [<.edr>]]
[-n [<.ndx>]] [-m [<.tex>]] [-nice <int>] [-vdwfac <real>]
[-bonlo <real>] [-bonhi <real>] [-[no]rmsd] [-tol <real>]
[-abstol <real>] [-[no]ab] [-lastener <string>]
DESCRIPTION
gmx check 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 its contents will be summarized.
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, gmx check provides a quick check for such problems.
The program can compare two run 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 of
a rough outline for a methods section for a paper.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-f2 [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s1 [<.tpr/.tpb/...>] (top1.tpr) (Input, Optional)
Run input file: tpr tpb tpa
-s2 [<.tpr/.tpb/...>] (top2.tpr) (Input, Optional)
Run input file: tpr tpb tpa
-c [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-e [<.edr>] (ener.edr) (Input, Optional)
Energy file
-e2 [<.edr>] (ener2.edr) (Input, Optional)
Energy file
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-m [<.tex>] (doc.tex) (Output, Optional)
LaTeX file
Other options:
-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
-[no]rmsd (no)
Print RMSD for x, v and f
-tol <real> (0.001)
Relative tolerance for comparing real values defined as
2*(a-b)/(|a|+|b|)
-abstol <real> (0.001)
Absolute tolerance, useful when sums are close to zero.
-[no]ab (no)
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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-check(1)
