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

Sebastian Stolzenberg stolzenberg.sebastian at gmail.com
Sat Jun 7 17:15:21 CEST 2008

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?

Thank you very much for your help,

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