gmx dump

Main Table of Contents VERSION 5.0.1


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


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 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>] ( (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