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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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