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
>protein?
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
better!
==========================================================
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
email: vkitzing_at_silia.mpimf-heidelberg.mpg.de
WWW:
http://amber.ch.ic.ac.uk/dev_archive/
Received on Wed Mar 10 1999 - 05:24:04 PST
