Thanks Michael. On Mon, Jun 22, 2015 at 3:50 PM, Michael Shirts <[email protected]> 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 <[email protected]> > 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 [email protected]. > > > -- > 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 [email protected]. > -- 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 [email protected].
