gmxcheck Main Table of Contents

VERSION 4.6.1 Tue 5 Mar 2013

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 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

Other options