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

aldi asmadi aldi.asmadi at gmail.com
Sun Feb 27 21:49:16 CET 2011

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

On Sun, Feb 27, 2011 at 11:34 PM, David van der Spoel
<spoel at 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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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