Interesting ...
do you have a reference for this?
XAvier.
On May 14, 2012, at 12:01 PM, Dommert Florian wrote:
On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote:
Hi,
You do not need to use the polarizable martini water model to
calculate the dipole of molecules. Or I am missing a point here!
g_dipole should do the work
XAvier.
Hi,
I want to point to another problem. If you simulate with a classical
force field, you usually have an effective set of partial charges.
This
means polarization effects are often included in the partial charges.
This in turn requires an appropriate calculation of the dipoles. A
simple sum over the charges, like g_dipole or g_current does, is not
sufficient. The true dipoles are only obtained, if the results from
the
MD are multiplied with a certain factor the is related to the
high-frequency limit of the dielectric constant, the electronic
dielectric constant. We have performed several studies on molecular
ionic liquids and showed, that with a set of bulk charges, the dipole
moments are reproduced correctly, if this electronic dielectric
constant
is taken into account appropriate. Also for water or any other
molecule,
the same arguments hold. For example, if TIP4P water is considered.
Calculating the dielectric constant gives a value around 50, which is
small compared to the exp. value of 80. However, if the correct
dipoles
are considered, a simulated value of around 80 is the result. Hence,
it
depends on the parametrization of the partial charges, how the dipole
moment or any related property has to be calculated.
If you are just interested in the static limit, an effective
description
with static partial charges is sufficient in my opinion. However, as
soon as you are also interested in the time behavior, like the
frequency
spectrum of the dielectric constant or conductivity, you consider the
electronic polarization explicitly with a corresponding force field,
as
Justin mentioned.
Cheers,
Flo
On May 13, 2012, at 15:11, dina dusti <dinadu...@yahoo.com> wrote:
Dear Justin,
Thank you very much from your response.
Best Regards
Dina
____________________________________________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: dina dusti <dinadu...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@gromacs.org>
Sent: Sunday, May 13, 2012 5:23 PM
Subject: Re: [gmx-users] dipole moment
On 5/13/12 8:41 AM, dina dusti wrote:
Dear GROMACS Specialists,
I have one system consists of water and two other molecules. I
work by MARTINI
CG force field. I want to calculate dipole moment of molecules in
water.
May I ask you to help me, Please?
I doubt you can. Unless you are using version 2.P of the force
field (which contains polarizable water), MARTINI uses a single,
uncharged particle to represent water. If there are no charges,
there is no dipole.
-Justin
-- ========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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