Yes I measured both, the density and the free volume using gromacs. Since the free volume changes with respect to time, shouldn’t the density also change with time ?
Thanks, Mohamed On Wed, May 6, 2020 at 08:23 David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: > > Hello everybody, > > > > I have two fundamental questions please. > > > > I have measured the fee volume and I discovered that, the free volume > > changes with respect to the time during the production run (different > value > > for each frame). However I have measured the density but the result does > > not change with respect to time. > > > > Shouldn't the density also changes with time if the free volume changes > > with time ? > > > > I also can't understand why the free volume changes with respect to the > > time, if the number of molecules and volume of box didn't change. > > > > Many Thanks, > > Mohamed > > > This is due to atomic fluctuations, that is they overlap more or less > depending on their distance, Did you use the freevolume tool in gromacs? > It may also depend on whether each freevolume calculations is converged > (-ninsert option). > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.org > -- > 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. > -- 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.