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,
----------------------------------------------------------------
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.ipst.umd.edu
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Received on Tue Aug 12 2003 - 20:53:00 PDT
