gmx-dump(1) GROMACS Manual gmx-dump(1)NAMEgmx-dump - Make binary files human readable
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 prob‐
lems.
The program can also preprocess a topology to help finding problems.
Note that currently setting GMXLIB is the only way to customize direc‐
tories 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-dump(1)
