gmx dump#


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


gmx dump reads a run input file (.tpr), a trajectory (.trr/.xtc/tng), an energy file (.edr), a checkpoint file (.cpt) or topology file (.top) and prints that to standard output in a readable format. This program is essential for checking your run input file in case of problems.


Options to specify input files:

-s <.tpr> (Optional)

Run input file to dump

-f <.xtc/.trr/…> (Optional)

Trajectory file to dump: xtc trr cpt gro g96 pdb tng

-e <.edr> (Optional)

Energy file to dump

-cp <.cpt> (Optional)

Checkpoint file to dump

-p <.top> (Optional)

Topology file to dump

-mtx <.mtx> (Optional)

Hessian matrix to dump

Options to specify output files:

-om <.mdp> (Optional)

grompp input file from run input file

Other options:

-[no]nr (yes)

Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)

-[no]param (no)

Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)

-[no]sys (no)

List the atoms and bonded interactions for the whole system instead of for each molecule type

-[no]orgir (no)

Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them

Known Issues#

  • The .mdp file produced by -om can not be read by grompp.