Is it an NPT simulation or NVT simulation? Arun On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal, <m.b.abdel...@gmail.com> wrote:
> 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. -- 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.
