[gmx-users] Parallel do_dssp analysis over mpi?

Erik Marklund erikm at xray.bmc.uu.se
Mon Nov 8 21:03:58 CET 2010

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


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

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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