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
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
[email protected] http://folding.bmc.uu.se/
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