[gmx-users] Parallel do_dssp analysis over mpi?

[Erik Marklund]

You can use the -b and -e flags to analyze parts of your trajectory and 
patch the results together afterwards.

Erik

Justin A. Lemkul skrev 2010-11-08 20.51:
>
>
> Ali Naqvi wrote:
>> Dear All,
>> I have a trajectory of 100ns and have been trying to analyze it using 
>> dssp program. I guess this question also goes for other analysis 
>> programs like g_rama, g_rdf and what not.
>>
>> Since the trajectory is big, it takes hours to analyze with do_dssp.. 
>> infact 48 hours. I have been able to analyse only one set of 100ns 
>> and have 7 more trajectories. Is it possible to get it running in 
>> parallel to expedite the analysis? If so, which flags need to be 
>> appended?
>>
>
> The only Gromacs program that is MPI-aware is mdrun.  Unless modify 
> the source code, then none of the other commands will run in parallel.
>
> -Justin
>
>> Cordially,
>> Ali
>>
>


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Erik Marklund, PhD student
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