Subject: RE: basic questions in MD

From: "Joseph Han" <josephh~at~stanford.edu>
Date: Thu, 19 Feb 2004 16:48:52 -0800

> -----Original Message-----
> From: Computational Chemistry List 
> [mailto:chemistry-request~at~ccl.net] On Behalf Of Jie Zheng
> Sent: Thursday, February 19, 2004 3:05 PM
> To: chemistry~at~ccl.net
> Subject: CCL:basic questions in MD
> 
> 
> Hi, CCLer:
>   I have a few basic questions for molecular dynamics.
>   1) why the system has to be neutral in molecular dynamics? From the
> numerial point of views, it seems that to be neutral or not does not
> affect the numerial algorithm. We still can get results. I 
> know there must
> have some physical meaning behind this, anybody can give a answer?

If the cell does not have a neutral change, then when you replicate it
using periodic boundary conditions, the total charge becomes infinity.
This does not make physical sense.

> 
>   2) why the cutoff distance can not larger than the 
> half-size of box? If
> we use the Ewald sum method to calculate nonbonded interactions, the
> system and its images have been extend to infinite. If we use 
> the cutoff
> method, the system is confined to the finite size by using periodic
> boundary conditon. My question is that if we extend our 
> simulation system
> to infinite as the Ewald sum does, the half-box cutoff is not 
> required for
> the simluation systems.

If the cutoff is greater than the half-size of the box, you will get
self-interaction errors.  Imagine a particle at the center of a cube.
Embed a sphere with a radius half the edge of the cube.  When you
replicate the cell, if the radius of the sphere is greater than this
size, it will interact with itself.

Joseph Han
Department of Chemical Engineering
Stanford University
650-723-0420
FAX:  650-725-7294