Questions and problems?
What dielectric constant with water?
Date: Thu, 9 Sep 1993 20:40:26 +0100 (BST)
From: K Bryson
Subject: Re: dielectric setting
To: amber@cgl.ucsf.EDU
On Thu, 9 Sep 1993, Dr. John M. Beale wrote:
I would very much appreciate receiving AMBER users' opinions on the
best way to set the dielectric multiplicative constant (DIELC) when
running simulations explicitly in water and using IDIEL=1 and periodic
boundary conditions. Assuming that the dielectric constant of water
is 80, how does one set up the simulation for this?
I find the dielectric in molecular simulations a rather
interesting object as well. The general concensus ( I believe )
is that if you've including water explicitly then you should be
using a dielectric of 1 since the explicit water will produce the
required dielectric of 80 on its own accord.
If you are not including explicit water then using a
straight dielectric of 80 ( ie, not distance dependent ) seems
to be invalid for three reasons.
-
It's a time averaged quantity.
That is the dielectric of water is frequency dependent
and hence should be different for different frequency motions.
-
It's a space averaged quantity, ie macroscopic.
So it shouldn't be applied between things only nm apart,
which is obvious in the limiting case of two atoms only
a few angstrongs apart and hence with a vacuum between them.
- Bound surface water around a protein does not have the
same dielectric as bulk water, so shouldn't be modelled
as such.
In the case of excluding explicit water the distance dielectric
model seems to be the most fashionable, but as a physicist I've
always been worried about a model that breaks Gauss' Law and
produces an unphysical model. But then if the model agrees with
enough experimental data, it's a good model !
On the distance dielectric model, for a particular protein BPTI,
Guenot and Kollman showed in a recent paper,
J. Comp. Chem, 14(3),295--311 (1993)
that the distance dielectric model with a finite cutoff provided
a closer average conformation to the explicit water model with
an infinite cut-off than did any of the explicit water models
with finite cut-offs.
So the distance dielectric model gets a vote of confidence.
Criticism, and the general exchange of knowledge over the
user group, on the above prose, would be most welcome.
----------~~~~~~------~~~~~~~~~~---------------~~~~~----------~~~~~--
K.Bryson email: kb7@tower.york.ac.uk
Biophysics Group Tel : +44 904 430000 Extn. 2236
Physics Department Fax : +44 904 432214
University of York
Heslington "Molecular modelling of DNA and its
YORK, UK interaction with small molecules."
YO1 5DD
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Date: Thu, 9 Sep 93 15:12:41 -0700
From: ross@cgl.ucsf.EDU (Bill Ross )
To: amber@cgl.ucsf.EDU
Subject: dielectric
Kevin Bryson writes:
The general concensus ( I believe )
is that if you've including water explicitly then you should be
using a dielectric of 1 since the explicit water will produce the
required dielectric of 80 on its own accord.
This is indeed the general concensus. I was thinking of how to
demonstrate it, and with Tom Cheatham's help came up with the
following idea:
Compare the axial forces on two ions at various fixed distances
in a vacuum with the electrostatic component of axial forces where
the ions are surrounded by water (over an MD run). Hopefully, the
forces in water should the same as for a dielectric of 80 in vacuum.
Such a test might not be conclusive for distances that we model, as
implied by Kevin Bryson's remarks.
Bill Ross
Web Masters <webadmin@www.amber.ucsf.edu>
Last modified: Tue Nov 15 18:50:29 1994
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