[gmx-users] Gromacs single sum virial calculation for periodic systems
julius.schulz at fu-berlin.de
Tue Jul 21 21:51:49 CEST 2015
> Am 21.07.2015 um 20:44 schrieb David van der Spoel <spoel at xray.bmc.uu.se>:
> On 21/07/15 17:32, Julius Schulz wrote:
>> I am trying to understand, how Gromacs calculates the virial for periodic systems. According to
>> Eq. B.11 in the Gromacs manual, this should be a function of the total forces of the particles.
>> However, I don't understand, how delta_i is being calculated.
>> As far as I can see it is basically defined in Eq. B.3. In Eq. B.11 it is used as if it would only
>> depend on the particle index i, however as defined in Eq. B.3 I would guess it should depend on both
>> i and j. An older thread on that matter referenced to the thesis of Henk Bekkers
>> (http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/, Chapter 2), however there the
>> second part of the virial is not simply a function of the total force on the individual particles
>> and the sums runs over all periodic images not over all particles.
>> Maybe someone can help me understanding this? Basically what I am after is, that I have an already
>> existing (expensive to compute) trajectory with forces for which I would like to obtain the virial.
>> Is this impossible?
> Are you aware of the mdrun -rerun option?
Yes, I know about this option, but actually it is a non-gromacs trajectory (some very expensive
to calculate ab-initio md trajectories I was given by a colleague). But since I am most familiar
with Gromacs, I’m using this as a testbed to get my calculation correct.
Therefore I’m looking for a way to calculate the virial using forces and positions (and velocities)
alone. The Gromacs Manual is basically the only place I found this single sum virial with pbc, thus
I was hoping to find an answer on this list. Eq. B.11 at least suggests to me, it should be possible,
or is this a misinterpretation of mine?
Thank you, Greetings, Julius
PS: Actually I think, the problem would even exist if it was a Gromacs trajectory, since I would need
individual pair forces, which would have to be recalculated during the rerun and this is what’s computionally
expensive, or am I mistaken? (I need full time resolution, so no frame skipping would be possible)
>> Greetings, Julius
>> Julius Schulz
>> FU Berlin, Fachbereich Physik,
>> AG Netz (room 0.3.30)
>> Phone (++49|0) 30-838-55279
>> Arnimallee 14
>> 14195 Berlin, Germany
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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