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

From: Margaret S. Cheung <>
Date: Tue, 12 Aug 2003 14:56:47 -0400 (EDT)

Dear amber users and developers,

I was wondering if anyone is willing to share how to get the diffusion
coefficient of particles when the periodic boundary conditions are
PS. I am not able to simulate my system without a periodic
boundary box; therefore, I am not able to use the einstein relation to
obtain the diffusion coefficient. 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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