Re: Counterions

From: Eberhard von Kitzing <>
Date: Wed 10 Mar 1999 14:24:04 +0100

Dear Rebecca Perlow,

At 1:07 Uhr +0100 10.03.1999, Rebecca Perlow wrote:
>I am doing an MD simulation of a large protein and DNA. The system
>overall has a significant negative charge. Should I use counterions to
>neutralize the system before running MD? What is the most accepted policy
>to follow regarding this issue?
>And if I do use counterions, shouldn't I just neutralize the system
>overall on the exterior? If the DNA is neutralized by itself beforehand,
>wouldn't that disrupt its important electroststic interactions with the

It is experimentally well known that DNA does not behave very well
if one tries to deplete it of all its ions. Thus at least neutrality
must be obtained to simulate a kind of "realistic" environment.

A second problem is that the relaxation time of the ion cloud is
inverse proportional to the concentration of excess ions. Maxwell's
relaxation time has the form:

     tMaxwell = lDH^2 / D

where D is the diffusion constant and lDH the Debye length.
One needs at least a single Maxwell relaxation time to equilibrate
the system. For 100 mM and typical ionic diffusion constants in
water this time is still in the order of ns. Thus, one M would be


Eberhard von Kitzing

Abteilung Zellphysiologie
Max-Planck-Institut fuer Medizinische Forschung
Jahnstr. 29
D 69120 Heidelberg Tel: +49 6221 486 467
Germany FAX: +49 6221 486 459

Received on Wed Mar 10 1999 - 05:24:04 PST
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