-----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart
Enemark Soeren wrote: > Dear all, > > I am trying to calculate diffusion coefficients for a system of (30) > glycine molecules in a box with (1000) water. > > > > After running: > > g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx > > > > I get a list of diffusion coefficients - one for each glycine molecule. > I then calculate the average and the stdev: > > > > Average=1.004 > > Stdev=0.7661 > > > > My problem is that the stdev is very great! More than +/- 75% of the > average value. > > Why is that? Short simulation most likely. Since these things are big it takes a long time to equilibrate. My simulation is 10ns long with xtc saved every 1 ps. I thought I had enough data!? How long is "long time"? > > > > Also, what is the reason for the trestart=10 default value? Shouldn't it > be better to have trestart=1, if my xtc file is saved every 1 ps? No, because there is correlation in the system. Ideally you would take this time to be longer than the correlation time. You could try to find an estimate of that from the velocity autocorrelation. So, I must run velocity autocorrelation to find out when the velocities become uncorrelated, and then use this time as my trestart? Thanks, Soren > > > > Thanks, > > Soren Enemark > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > 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. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
