[gmx-users] Parallel do_dssp analysis over mpi?

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 8 21:05:22 CET 2010

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

But does that really save time?  Patching .xpm files is not entirely 
straightforward.  Might end up taking a lot more time :)


> 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


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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