Hi Michael, Has problem been solved about molecules drifting in md-vv integrator? Also can you please check my potential energy second pic in http://imgur.com/6aJkRoQ&fjXGmXu#0 . <http://imgur.com/6aJkRoQ&fjXGmXu#0> What could be the reason this big jump in potential energy (integrator : md-vv)? And why I do not see the same jump by using md integrator?
thanks in advance <http://imgur.com/6aJkRoQ&fjXGmXu#0> On Mon, Jun 22, 2015 at 6:22 PM, gozde ergin <gozdeeer...@gmail.com> wrote: > Hi Michael, > > There is one more question, I still could not get why do I see that big > jump in potential energy? > I understand all bulk is drifting in the box because of the COM removal > step is omitted for md-vv but how this issue can effect the potential > energy? > > best > > On Mon, Jun 22, 2015 at 4:05 PM, gozde ergin <gozdeeer...@gmail.com> > wrote: > >> Thanks Michael. >> >> On Mon, Jun 22, 2015 at 3:50 PM, Michael Shirts <mrshi...@gmail.com> >> wrote: >> >>> At some point, a COM removal step was omitted for md-vv. A change has >>> been >>> proposed in in gerrit for a while (See >>> https://gerrit.gromacs.org/#/c/4649/ >>> and https://gerrit.gromacs.org/#/c/4467/ ), but one of the developers >>> asked >>> to have the source of the problem traced to understand better what >>> happened >>> and fixed at that point and merged forward. Hopefully this can get sorted >>> out later this week. >>> >>> >>> On Mon, Jun 22, 2015 at 9:10 AM, gozde ergin <gozdeeer...@gmail.com> >>> wrote: >>> >>> > Hi all, >>> > >>> > >>> > I was using md-vv as an integrator however I discovered that all bulk >>> was >>> > moving (drifting) during the simulation. >>> > >>> > Than I changed the integrator and used md. The bulk molecules did not >>> move >>> > during the simulation, just stayed in the middle of box. >>> > >>> > I attached the potential and kinetic energies of the systems with >>> md-vv and >>> > md integrator. >>> > >>> > http://imgur.com/6aJkRoQ&fjXGmXu#0 >>> > >>> > >>> > When I use md-vv other than drifting, I also saw big jump in potential >>> > energy after 10ns. However this is not the case for md integrator >>> system. >>> > >>> > Is this normal? >>> > Does anyone face with the same problem? >>> > What could be the reason for that? >>> > >>> > thanks in advance. >>> > -- >>> > 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.