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gmx-dump - Online in the Cloud

Run gmx-dump in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmx-dump that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-dump - Make binary files human readable

SYNOPSIS


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

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