Provided by: gromacs-data_2023.3-1ubuntu3_all 
NAME
gmx-check - Check and compare files
SYNOPSIS
gmx check [-f [<.xtc/.trr/...>]] [-f2 [<.xtc/.trr/...>]] [-s1 [<.tpr>]]
[-s2 [<.tpr>]] [-c [<.tpr/.gro/...>]] [-e [<.edr>]]
[-e2 [<.edr>]] [-n [<.ndx>]] [-m [<.tex>]] [-vdwfac <real>]
[-bonlo <real>] [-bonhi <real>] [-[no]rmsd] [-tol <real>]
[-abstol <real>] [-[no]ab] [-lastener <string>]
DESCRIPTION
gmx check reads a trajectory (.tng, .trr or .xtc), an energy file (.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) files when both -s1 and -s2 are supplied. When comparing run
input files this way, the default relative tolerance is reduced to 0.000001 and the absolute tolerance
set to zero to find any differences not due to minor compiler optimization differences, although you can
of course still set any other tolerances through the options. 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.
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng
-f2 [<.xtc/.trr/...>] (traj.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng
-s1 [<.tpr>] (top1.tpr) (Optional)
Portable xdr run input file
-s2 [<.tpr>] (top2.tpr) (Optional)
Portable xdr run input file
-c [<.tpr/.gro/...>] (topol.tpr) (Optional)
Structure+mass(db): tpr gro g96 pdb brk ent
-e [<.edr>] (ener.edr) (Optional)
Energy file
-e2 [<.edr>] (ener2.edr) (Optional)
Energy file
-n [<.ndx>] (index.ndx) (Optional)
Index file
Options to specify output files:
-m [<.tex>] (doc.tex) (Optional)
LaTeX file
Other options:
-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 ALSO
gmx(1)
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2023, GROMACS development team
2023.3 Oct 19, 2023 GMX-CHECK(1)