gmx-dump man page

gmx-dump — 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]

Description

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

Known Issues

See Also

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

Referenced By

gmx(1).

Mar 21, 2018 2018.1 GROMACS