gmx-dump - Man Page

Make binary files human readable

Synopsis

gmx dump [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-e [<.edr>]]
         [-cp [<.cpt>]] [-p [<.top>]] [-mtx [<.mtx>]] [-om [<.mdp>]]
         [-[no]nr] [-[no]param] [-[no]sys] [-[no]orgir]

gmx dump reads a run input file (.tpr), a trajectory (.trr/.xtc//tng), an energy file (.edr) or a checkpoint file (.cpt) and prints that to standard output in a readable format. This program is essential for checking your run input file in case of problems.

The program can also preprocess a topology to help finding problems. Note that currently setting GMXLIB is the only way to customize directories used for searching include files.

Options

Options to specify input files:

-s [<.tpr>] (topol.tpr) (Optional): Portable xdr run input file
-f [<.xtc/.trr/…>] (traj.xtc) (Optional): Trajectory: xtc trr cpt gro g96 pdb tng
-e [<.edr>] (ener.edr) (Optional): Energy file
-cp [<.cpt>] (state.cpt) (Optional): Checkpoint file
-p [<.top>] (topol.top) (Optional): Topology file
-mtx [<.mtx>] (hessian.mtx) (Optional): Hessian matrix

Options to specify output files:

-om [<.mdp>] (grompp.mdp) (Optional): grompp input file with MD parameters

Other options:

-[no]nr (yes): Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)
-[no]param (no): Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)
-[no]sys (no): List the atoms and bonded interactions for the whole system instead of for each molecule type
-[no]orgir (no): Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them