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

Julius Schulz julius.schulz at fu-berlin.de
Tue Jul 21 17:32:08 CEST 2015

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?

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
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