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Man Pages


Manual Reference Pages  -  GMX-DUMP (1)

NAME

gmx-dump - Make binary files human readable

CONTENTS

Synopsis
Description
Options
Known Issues
See Also

SYNOPSIS

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

DESCRIPTION

gmx dump reads a run input file (.tpa/.tpr/.tpb), a trajectory (.trj/.trr/.xtc), an energy file (.ene/.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 and output files:

-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Run input file: tpr tpb tpa

-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng

-e [<.edr>] (ener.edr) (Input, Optional)
Energy file

-cp [<.cpt>] (state.cpt) (Input, Optional)
Checkpoint file

-p [<.top>] (topol.top) (Input, Optional)
Topology file

-mtx [<.mtx>] (hessian.mtx) (Input, Optional)
Hessian matrix

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

Other options:

-nice <int> (0)
Set the nicelevel

-[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

gromacs(7)

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

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VERSION 5.0.6 GMX-DUMP (1)

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