gmx dump¶
Synopsis¶
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]
Description¶
gmx dump reads a run input file (.tpr),
a trajectory (.trr/.xtc//tng), an energy
file (.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 files:
-s[<.tpr>] (topol.tpr) (Optional)- Portable xdr run input file
-f[<.xtc/.trr/…>] (traj.xtc) (Optional)- Trajectory: xtc trr cpt gro g96 pdb tng
-e[<.edr>] (ener.edr) (Optional)- Energy file
-cp[<.cpt>] (state.cpt) (Optional)- Checkpoint file
-p[<.top>] (topol.top) (Optional)- Topology file
-mtx[<.mtx>] (hessian.mtx) (Optional)- Hessian matrix
Options to specify output files:
-om[<.mdp>] (grompp.mdp) (Optional)- grompp input file with MD parameters
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¶
- Position restraint output from -sys -s is broken