[gmx-users] md-vv and md

[gozde ergin]

Thanks Michael.

On Mon, Jun 22, 2015 at 3:50 PM, Michael Shirts <mrshirts at 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 <gozdeeergin at 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.
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