Re: [AMBER] calculation diffusion coefficient

From: David A Case <>
Date: Sun, 1 Jun 2014 07:37:50 -0400

On Sun, Jun 01, 2014, Sohag Biswas wrote:

> I need your help. I am trying to calculate mutual diffusion coefficient. My
> system contains 600 wat residue and 600 DMF residue. During calculation I
> am using this following command.
> diffusion :1-1200 8 average 0.50diff
> it is calculating, after that i am following manual to calculate diffusion.
> My question which equation it is following during mutual diffusion
> coefficient calculation? please help me. Thanks.

The "diffusion" command only works for "self" or "tagged" diffusion, following
the movements of a single molecule (then averaging the results over the the
molecules in the mask). It does not do the sort of analysis you requesting.


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Received on Sun Jun 01 2014 - 05:00:03 PDT
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