Yang Ye wrote: > 1. how long is the simulation? > 2. did you start from equilibration (with gen_vel=yes) or production md? > 3. ... > > On 12/5/2007 8:28 PM, Dechang Li wrote: >> Dear all, >> >> I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). >> I run two similar simulations, one for 2 cpus, while the other for 16 cpus. >> The two simulations have the same .gro, .top, and the same .mdp files. I >> found >> the results were not the same. In the 2 cpus simulation, the two proteins >> run closer and closer. But they run apart in the 16 cpus simulation. >> Is that normal the different results when using different number cpus? >> The >> size of my simulation box is 9*7*7.
Answer is yes. http://wiki.gromacs.org/index.php/Reproducibility >> >> >> >> >> >> >> >> Best regards, >> >> 2007-12-5 >> >> >> ========================================= >> Dechang Li, PhD Candidate >> Department of Engineering Mechanics >> Tsinghua University >> Beijing 100084 >> PR China >> >> Tel: +86-10-62773779(O) >> Email: [EMAIL PROTECTED] >> ========================================= >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
