AMBER Archive (2003)

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

From: Margaret S. Cheung (mscheung_at_ipst.umd.edu)
Date: Tue Aug 12 2003 - 14:46:24 CDT

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. 

-- 
Sincerely,
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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         |  http://glue.umd.edu/~mscheung
College Park, MD 20742-2431    |  email: mscheung_at_ipst.umd.edu
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