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

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.

1. It's a time averaged quantity. That is the dielectric of water is frequency dependent and hence should be different for different frequency motions.
2. 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.
3. Bound surface water around a protein does not have the same dielectric as bulk water, so shouldn't be modelled as such.

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             
 -------------------~~~~~-------------~~~~--------~~~~--------~~~~~---

Date: Thu, 9 Sep 93 15:12:41 -0700
From: ross@cgl.ucsf.EDU (Bill Ross )
To: amber@cgl.ucsf.EDU
Subject: dielectric

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