NAME

       gmxcheck - checks and compares files

       VERSION 4.6.5

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 -[no]version -nice int -vdwfac real -bonlo real -bonhi  real  -[no]rmsd  -tol
       real -abstol 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 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,  gmxcheck 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.

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

       -e2 ener2.edr Input, Opt.
        Energy file

       -n index.ndx Input, Opt.
        Index file

       -m doc.tex Output, Opt.
        LaTeX file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version 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

       -[no]rmsdno
        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]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/>.

                                                 Mon 2 Dec 2013                                      gmxcheck(1)