table of contents
GMX-DUMP(1) | GROMACS | GMX-DUMP(1) |
NAME¶
gmx-dump - Make binary files human readableSYNOPSIS¶
gmx dump [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-e [<.edr>]] [-cp [<.cpt>]] [-p [<.top>]] [-mtx [<.mtx>]] [-om [<.mdp>]] [-[no]nr] [-[no]sys]
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]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
SEE ALSO¶
gmx(1)More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT¶
2016, GROMACS development teamOctober 28, 2016 | 2016.1 |