[gmx-users] Parallel do_dssp analysis over mpi?

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 8 20:51:02 CET 2010

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.


> Cordially,
> Ali


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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