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]sys]

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]sys (no)

List the atoms and bonded interactions for the whole system instead of for each molecule type

Known Issues

  • Position restraint output from -sys -s is broken

See Also

gmx(1)

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

Referenced By

gmx(1).

Mar 13, 2017 2016.3 GROMACS