[gmx-users] Gromacs single sum virial calculation for periodic systems

David van der Spoel spoel at xray.bmc.uu.se
Tue Jul 21 20:44:47 CEST 2015

On 21/07/15 17:32, Julius Schulz wrote:
> Hello,
> 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?
> 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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