[gmx-users] PME, epsilon_rf and dielectric constant calculation
David van der Spoel
spoel at xray.bmc.uu.se
Thu Mar 8 09:44:44 CET 2007
Itamar Kass wrote:
> Dear Mark,
> I read the manual few times looking for a clue. The only thing I could
> understand it that epsilon_rf is not taking inti account if I don't use
> reaction field.
> Best, Itamar.
> Mark Abraham wrote:
>>> Dear all,
>>> I wish to calculate the dielectric constant of small molecules liquids.
>>> In order to do so, I am simulating the system using PME, with epsilon_r
>>> = 1.
>>> I have few questions:
>>> 1. What is the meaning of epsilon_rf when I am using PME, if it
>>> important, what it should be?
>> Have you looked in section 7.3?
>>> 2. Whet is the best way to calculate the dielectric constant of the
>>> simulation box, does g_dipole is enough or should I use g_dielectric
You need to use g_dipoles -epsilonRF 0 if you have used defaults for
PME. If you have used another
dielectric for PME (epsilon_surface) then you need to change that in the
input to g_dipoles as well.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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