debian man page for gmxcheck

gmxcheck(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       gmxcheck(1)

NAME
       gmxcheck - checks and compares files

       VERSION 4.5.4-dev-20110404-bc5695c

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]ver-
       sion -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 infor-
       mation 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 4 Apr 2011						       gmxcheck(1)