Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions.

From: David A. Case <>
Date: Tue, 12 Aug 2003 12:23:55 -0700

On Tue, Aug 12, 2003, Margaret S. Cheung wrote:
> I was wondering if anyone is willing to share how to get the diffusion
> coefficient of particles when the periodic boundary conditions are
> included.

As long as you don't "wrap" or "image" your results, an ordinary analysis
(calculating the mean square movement as a function of time) should work.
In this manner, there is no direct influence of the periodicity on the result,
e.g. the mean square displacement will continue to rise indefintely. There
would still be an "indirect" effect from the fact that there are artifactual
particle-particle correlations at distances comparable to the box size.
As far as I know, the only way to remove the latter is to go to progressively
larger box sizes.

For most biomolecular simluations, errors in translation diffusion caused by
limitations in the potential functions often swamp any artifacts caused by

..not sure if this really answers your question or not....dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Tue Aug 12 2003 - 20:53:00 PDT
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