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

Sebastian Stolzenberg stolzenberg.sebastian at gmail.com
Sun Jun 8 00:54:55 CEST 2008

Thank you, David,

 >> mdrun -multi comes closest, but you have to generate 100 tpr files first

Still interesting, I haven't used Gromacs so far.
So this is still ONE Gromacs run, I just have produce 100 tpr files first?
You already see that I am most worried about the initial overhead of an 
MD run.


David van der Spoel wrote:
> 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?
> no.
> 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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