[gmx-users] Parallel do_dssp analysis over mpi?

[Justin A. Lemkul]

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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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