I had the same problem before. I think the best way to do it is to analyze every group separately.
On Mon, Apr 20, 2009 at 1:53 AM, Borys Szefczyk <szefc...@mml.ch.pwr.wroc.pl> wrote: > Dear Gromacs users, > > I'm doing some tests on molten sodium chloride, trying to calculate > self-diffusion coefficients of both ions. Could someone tell me what > actually does the -ngroup switch of the g_msd program? > > When I compute D for chlorine only, I get 6.4607e-5 cm^2/s; > for sodium only, I get D = 9.0996e-5 cm^2/s. > > But when I set -ngroup to 2 and specify both groups (NA and CL) > subsequently, I get: > D[ NA+] = 9.0976e-5 cm^2/s > D[ CL-] = 0.9128e-5 cm^2/s > Plot of MSD looks fine for NA, but not for CL - it's a saw-shaped, > almost flat line. > > If I enter the groups in reverse order, first CL, then NA, I get: > D[ CL-] = 6.4607e-5 cm^2/s > D[ NA+] = 4.2326e-5 cm^2/s > Again, first plot look fine, the second - not. > > Why these results differ? > > Regards, > Borys Szefczyk > > > -- > REQUIMTE, & Molecular Modelling & Quantum Chemistry Group, > Department of Chemistry, & Institute of Physical & Theoretical Chemistry, > Faculty of Science, & Wroclaw University of Technology > University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk > _______________________________________________ > gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php