gmxcheck VERSION 3.3_beta_20050823

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 -[no]h -nice int -vdwfac real -bonlo real -bonhi real -tol real -lastener string

gmxcheck reads a trajectory ( .trj , .trr or

.xtc ) or an energy file ( .ene or .edr ) 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).

-f traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb

-f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb

-s1 top1.tpr Input, Opt. Generic run input: tpr tpb tpa xml

-s2 top2.tpr Input, Opt. Generic run input: tpr tpb tpa xml

-c topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb xml

-e ener.edr Input, Opt. Generic energy: edr ene

-e2 ener2.edr Input, Opt. Generic energy: edr ene

-n index.ndx Input, Opt. Index file

-[no]h no 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|)

-lastener string Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.