Subject: Re: CCL:InsightII, PBC, counter ions

From: Eberhard von Kitzing <[email-masked]>
Date: Mon, 6 Dec 1999 09:09:38 +0100

Dear CCLler,

At 16:55 Uhr +0100 03.12.1999, Jianhui Wu wrote:
>I am trying to model ligand-protein interaction using discovery within
>InsightII (version 97). I would like to solvate the system by PBC water
>box.
>The protein has –12 charge (ligand is neutral). Is it essential to add
>the counter
>ions in the system to neutralize the net charge before a PBC discovery
>calculation (MM or MD) is performed?  (Probably, yes)

The Maxwell relaxation time (see introductions into semi conductor
physics) is the time needed by the system to equilibrate. It is
in the order of lDH^2/D where lDH is the Debye length and D the
diffusion constant of the ions. Thus, to add salt in addition to
the excess charge would improve the equilibration of your simulation.
Test calculations done by others showed that such additional salt
generally stabilizes the simulation.

==========================================================

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: [email-masked]
WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/