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
also.
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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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