[gmx-users] A few general questions on Gromacs

Mark Abraham mark.abraham at anu.edu.au
Tue Jun 26 16:19:29 CEST 2007

> Hi,
> I would like to thank you and David for the answers. By "multiple
> programs",
> I meant batch scripts that contain other preprocessing/postprocessing
> programs besides mdrun  (like grompp, pdb2gmx,...) - so this would be a
> case
> in which the processing is done in multiple steps. I asked this because
> we're especially interested in multi-step processes (workflows); and in
> the
> Gromacs tutorials most of the examples are like this (some other programs
> are invoked before and after mdrun).

Well a typical replica-exchange MD workflow for me includes a script that
takes some PDB file with the right protein configuration, and runs
pdb2gmx, editconf, genion and grompp using expect and various command line
flags to generate files suitable for starting equilibrations. These tend
to get run in multiple batch scripts, then another script to make the
simulation run input files. Then a batch script that runs a simulation,
optionally using tpbconv to create continuation run input files as
required, and resubmits a copy of itself afterwards at the end, to create
an infinite loop until user interaction or machine crash intervenes.


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