question on a chared system MD simulation

From: Hyonseok Hwang (
Date: Sun Jun 06 2004 - 18:05:35 CDT

Dear all,

My system is composed of one sodium cation embedded in a small protein
tube (the cation always resides in the protein) and water molecules. I
use PME method for the coulomb potential. Since I made restraints in
z-direction for the protein and cation, they can move freely only in x
and y directions. The thing I noticed is that as the simulation goes,
the cation and the protein which surrounds the cation tend to go to the
edge of the simulation box. (box is a cube) I'm wondering if this is
caused by the image charge due to the periodic boundary condition. What
I mean is that since the cation sees image charges around it and the
distance between the cation and the image charges are the farthest when
the cation goes to the edge, it could go to the edge of the simulation
box. Is this true? if this is true, could you let me know how to solve
this problem, please?

Thank you very much.


Hyonseok Hwang
Postdoctoral Fellow
Department of Chemistry
Northwestern University
2145 Sheridan Rd.
Evanston, IL 60208-3113 USA

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