Re: [gmx-users] Free volume variation during the simulation
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 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 > > 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.
Re: [gmx-users] Free volume variation during the simulation
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 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.
Re: [gmx-users] Free volume variation during the simulation
I started with NVT then NPT then md production run. Thanks, Kohamed On Wed, May 6, 2020 at 10:40 Arun Srikanth wrote: > Is it an NPT simulation or NVT simulation? > Arun > > On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal, > 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 > > 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. -- 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.
Re: [gmx-users] Free volume variation during the simulation
Is it an NPT simulation or NVT simulation? Arun On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal, 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 > 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.
Re: [gmx-users] Free volume variation during the simulation
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 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.
Re: [gmx-users] Free volume variation during the simulation
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.
Re: [gmx-users] Free volume variation during the simulation
I am simulating Crystal System (C60 molecules) Thanks, Mohamed On Wed, May 6, 2020 at 1:22 AM Arun Srikanth wrote: > Are you simulating a crystal or amorphous system? > > Arun > > On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal > wrote: > > > 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 > > -- > > 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.
Re: [gmx-users] Free volume variation during the simulation
Are you simulating a crystal or amorphous system? Arun On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal wrote: > 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 > -- > 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.