On 2011-02-27 21.49, aldi asmadi wrote:
Many thanks David.
Just want to confirm that I understand how to calculate the monomer
correctly. So I put the single molecule inside a large cubic box, say
with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the
same cut-off parameters as the ones that I apply during my bulk
simulation?
Infinite cutoff is best, since you probably use PME in bulk but can not
do that in gas phase. If you are using the Charmm parameters I'm pretty
sure they have published DHvap values so you can compare.
On Sun, Feb 27, 2011 at 11:34 PM, David van der Spoel
<sp...@xray.bmc.uu.se> wrote:
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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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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