[gmx-users] Question on energygrps setting
Dear users, I know interaction energy calculation is carried out via energygrps setting in mdp file. Because free energy-related settings do not include this energygrps setting, so I think this energygrps setting may NOT be related to free energy settings. Could I ask whether my idea is correct or not? Thanks! Lei -- 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.
[gmx-users] Info regarding restrained minimization, equilibration & production
Dear Gromacs users, I am interested on studying the interaction between large metal cluster anions (polyoxometallates, POM) with different organic cations (e.g perylenes, etc..) in water. I have already the non bonded parameters of POMs from literature, while the bonded parameters I calculated from Gaussian and VFFDT software. If I do not apply a position restraining force on the POM atoms, the POM structure gets distorted too much from the experimental one. I guess this is due to the lack of a good force field parametrization for metal-containing compound. *Thus, my question is the following:* *can I keep applying a position restraining force on POM atoms during the minimization, equilibration and production steps or is it conceptually wrong?* Thanks. Best regards, Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
