Main Table of Contents

Wed 13 Nov 2013


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

Other options

-[no]h bool no Print help info and quit
-[no]version bool no 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]rmsd bool no 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]ab bool no 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.