Synopsis
gmx dump [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]] [-e [<.edr>]]
[-cp [<.cpt>]] [-p [<.top>]] [-mtx [<.mtx>]] [-om [<.mdp>]]
[-nice ] [-[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
