Thanks david for your reply. Can you tell me up to how many -np value current version of GROMACS can be optimized (or will reduce the simulation time) ?
Also, how can I test the accuracy of my process when I can't get same result with similar option (while scaling )? With Thanks, Vivek 2008/9/11 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wrote: > >> Hi There, >> I am running gromacs parellal version on cluster, with different -np >> options. >> On analyzing the 5 nsec trajectory using ngmx, I am finding difference in >> the trajectory of two similar runs (only thing varying in two runs in -np >> i.e 20 and 64 ), where mdp file and input files are same in two cases. >> I am wondering why I am getting this difference in two trajectories ? >> I am looking for the advice whether I did something wrong or what may be >> the probable reason for this difference. >> > > THis is normal. > > In a computer (a+b)+c is not equal to a+(b+c). > > > Also, I am not able to run gromacs faster by increasing the -np issue, Is >> there any max limit for scaling gromacs on parellal cluster ? >> >> This will be fixed in 4.0 > > > > With Thanks, >> Vivek >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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., Professor of Biology > 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 >
_______________________________________________ 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
