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

       2020, GROMACS development team