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

From: Margaret S. Cheung <>
Date: Tue, 12 Aug 2003 15:46:24 -0400 (EDT)

Dear Dr. Case,

Thank you for your prompt reply.
> 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

Does it mean that I keep track of a particle and reinstate its random walk
in space and time such that the displacement between any time step will
not reflect a size of the box?

> 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
> PBC's.

Thank you for bringing this up. Actually my simulations are also roubled
by this kind of translational diffusion. Is there any way to get rid of
this? Thank you.

Margaret S. Cheung,  Ph. D.    |  IPST UMCP Tel: (301)405-7568
Postdoctoral Fellow            |  IPST UMCP Fax: (301)314-9404
IPST  Room 2116                |  NCBI NIH  Tel: (301)402-9527
University of Maryland         |
College Park, MD 20742-2431    |  email:
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Received on Tue Aug 12 2003 - 20:53:00 PDT
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