[gmx-users] md-vv and md

[Michael Shirts]

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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