Dear All, Say I want to calculate how the water molecules near the surface of protein are diffusing, how would I do that? Say I look at some hydrogen bonding interactions using VMD and zoom in and identify the SOL molecules around the surface . Can I create an index file containing those particular SOL molecules and calculate their diffusion? Would this work or is there another proper way to do it than just identifying such solvent molecules visually?
Thanks, Regards Apramita -- 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.
