Many thanks david for the explanation. In did NVT then NPT equilibiration and then the production run, in the production run .mdp file I have the same parameters as in NVT and NPT.mdp files. Does this mean that my simulation is a NVT simulation or NPT ?
Is it possible to do only one of them (NVT or NPT) equilibiration ? I thought that I must do both of them before I start the final production run. Thanks again, Mohamed On Wed, May 6, 2020 at 12:50 PM David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Den 2020-05-06 kl. 10:21, skrev Mohamed Abdelaal: > > 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 ? > What do you mean with "changes"? If the density is constant (with > fluctuations) in an equilibrium NPT simulation then the free volume > should fluctuate around an average as well. > > If you have a NVT simulation on the other hand, the total density is > going to be constant, but if your system undergoes a phase change the > freevolume will change. > > > > 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. > >> > > > -- > 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.
