Provided by: gromacs-data_4.6.5-1build1_all bug


       gmxcheck - checks and compares files

       VERSION 4.6.5


       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


         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.


       -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


        Print help info and quit

        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

        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.

        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.



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                              gmxcheck(1)