[gmx-users] md-vv and md

[gozde ergin]

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.
>> > --
>> > 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-request at 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-request at gromacs.org.
>>
>
>