> Using g_msd on a group of atoms results in an msd vs. time plot which is > the result of an average over all the atoms' motions. I would like to > obtain the same plot, but for an average over the center of mass motions > of a group of molecules. Using the -mol option results in a plot of the > diffusion coefficient for each individual molecule. Do I need to use > the -mw option for each molecule seperately and then average them > together myself? Thank you for any ideas. It seems that because MSDs of separate atoms are mostly very close to those of the center-of-mass GROMACS developers has made the latter case default. Using the '-mol' of g_msd option should give you a diffusion constant of the center-of-mass (besides that graph)...
I'm not sure, however. It's also a good idea to examine a programme code. :) -- Vitaly V. Chaban School of Chemistry University of Kharkiv Svobody sq.,4 Kharkiv 61077, Ukraine _______________________________________________ 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
