[gmx-users] md-vv and md

[gozde ergin]

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 <gozdeeergin at 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 <gozdeeergin at gmail.com>
> wrote:
>
>> 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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>>
>