Hi GMX users: I did a simulation of a bilayer, and I would like to calculate the diffusion coefficent of lipids by g_msd command.
I used the following command: g_msd -s *.tpr -f *.xtc -n index.ndx -beginfit xx -endfit xx -trestart xx -o msd.xvg I have 144 lipids in one leaflet. I am wondering what is the msd plot I got. To my understanding, the MSD was calculated based on the move of the center of mass of each lipid molecular, right? Or the MSD was calculated based on the move of all of the atoms I selected? There is an option -ngroup, what does this option mean? Thanks very much, I am really appreciate for any help. Cheers, RXG -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
