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NAME

       gmxcheck - checks and compares files

       VERSION 4.0.1

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
       -nice  int  -vdwfac  real  -bonlo  real  -bonhi  real -tol 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 it’s contents will be sumamrized.

       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  run two 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 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: edr ene

       -e2 ener2.edr Input, Opt.
        Energy file: edr ene

       -n index.ndx Input, Opt.
        Index file

       -m doc.tex Output, Opt.
        LaTeX file

OTHER OPTIONS

       -[no]hno
        Print help 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

       -tol real 0.001
        Relative   tolerance   for   comparing   real   values   defined    as
       2*(a-b)/(|a|+|b|)

       -[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/>.

                                Thu 16 Oct 2008                    gmxcheck(1)