Semen Esilevsky wrote:
Dear All,
I've found that the dielectric constant of pure SPC water according to
g_dipoles is only 3.94, which is obviously wrong!
I simulated the box of ~1500 SPC waters at 325 K and computed epsilon with
g_dipoles -temp 325
That's what I get:
Finite system Kirkwood g factor G_k = 0.190603
Infinite system Kirkwood g factor g_k = 0.143163
Epsilon = 3.94756
After some googling I've found that eps=65 for SPC model. So, what is wrong? Is
there any other way of computing epsilon?
first, it is T dependent, second you have to give extr options,
depending on how you did the simulation. g_dipoles -h
(hint look at the epsilonRF option). If you used a cut-off then you will
not get the right dielectric.
Sincerely,
Semen
----- Original Message ----
From: David van der Spoel <sp...@xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Wednesday, December 24, 2008 6:01:38 PM
Subject: Re: [gmx-users] g_dipoles questions
Semen Esilevsky wrote:
Dear David,
Thank you for reply! However there are still some question:
Dear All,
I have few questions about g_dipoles, which are not explained in the manual:
1) What method is used to calculate the epsilon? Is there a reference which can
be cited? Is it suitable for water solutions?
In principle it is suitable for solutions of neutral molecules only.
So, it should work for SPC water for example?
yes.
I'm confused by the phrase in the man page "you can compute e.g. the dielectric constant for
low dielectric media". What is "low"? Does it mean that the method works for, say,
benzene but not for water?
anything of neutral molecules.
The references are to Neuman papers from the 1980s.
Could you please give a little bit more detailed citation? Neuman is a
widespread name and 1980s is 10 years... At least a title or some keywords are
needed to find these papers.
check my 1998 JCP paper, the ref is given in g_dipoles.
Sincerely,
Semen
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________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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phone: 46 18 471 4205 fax: 46 18 511 755
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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