Dear Gromacs Users, I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know the diffusion constant of a particular cholesterol molecule. Towards this, I performed a g_msd using the command as follows-
g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 800000 -n index.ndx -mol chol.xvg where index.ndx contains a single index for the cholesterol atoms in question. In the end, I got 2 different values of diffusion constant, with one of them being displayed on the terminal screen and the other value in the chol.xvg file. Does anyone have any idea as to which value should be taken as the value of diffusion constant? Any help would be appreciated. Thank you! -- Best Regards, Ganesh Shahane -- 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.
