gmxdump_d1
Make binary files human readable
Part of gmx-dump(1).
Usage
gmx dump
[-s
[<.tpr/.tpb/ ...
>]]
[-f
[<.xtc/.trr/ ...
>]]
[-e
[<.edr>]]
[-cp
[<.cpt>]]
[-p
[<.top>]]
[-mtx
[<.mtx>]]
[-om
[<.mdp>]]
[-nice
<int>]
[-
[no]
nr]
[-
[no]
sys]
Overview
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
Releases
4 releases since Debian 5.0 (Lenny); the text changed 3 times.