[gmx-users] Positive potential energy in simulation using polarizable model

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 27 21:34:44 CET 2011

On 2011-02-27 21.20, aldi asmadi wrote:
> Dear all,
> This may sound obvious and normally I would know how to address the
> following question.  However, I would like to ask for your opinion.
> If we are simulating bulk liquid of hydrocarbon using the shell
> polarizable model, is it possible to have a positive value for the
> potential energy?  In my simulation, for every step, the system is
> energy minimized in order to accommodate the behavior of the shell
> particles.  For the shell particles, I use emtol = 0.1 and niter =
> 100.  In the log file, the potential energies are mostly reported as
> positives (except in the beginning steps), but there is no line saying
> that the 'energy minimization (EM) does not converge'.
> I understand that if the potential energy is positive, this may
> indicate that the system is exploding.  When I calculate the density,
> however, it corresponds quite well.
> Many thanks in advance.
> Regards,
> Aldi
You should subtract the energy of a monomer in order to get the 
intermolecular energy. Try computing the heat of vaporization:

DHvap = Epot(g) - Epot(l) + kBT

and compare it to the experimental value.

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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