[gmx-users] multiple MD runs within ONE MD script

David van der Spoel spoel at xray.bmc.uu.se
Sat Jun 7 18:51:17 CEST 2008

Sebastian Stolzenberg wrote:
> Hi everybody,
> (how) is it possible to write a single Gromacs MD script doing the following:
> 1.) Given a trajectory file (with say 100 frames), the MD script
> takes each of these 100 frames as initial structures for short MD
> runs, say 40fs.
> 2.) It determines some order parameter, maybe also determines an
> average, and outputs the data into a seperate
> external file.
> I am mostly interested in point 1.)
> I know, there is a quick and dirty shell script way of doing this, but
> is it possible doing this also within one single Gromacs run?

mdrun -multi comes closest, but you have to generate 100 tpr files first.
> Thank you very much for your help,
> Regards,
> Sebastian
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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