AMBER Archive (2009)

Subject: Re: [AMBER] deffision coefficient

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Apr 06 2009 - 21:16:39 CDT

On Tue, Apr 07, 2009, Nancy wrote:

> I am sorry to send this letter again,because no body answer my
> question.

Usually, when no answer is posted, it means that there is no simple
answer.

> I want to calculate diffusion coefficient of water in carbon
> nanotubes(amber10 , in explicit solvent ),

There have been a number of calculations of diffusion constants in ion
channels, so the same general ideas probably apply to nanotubes. The
means of analysis, and the ways in which such values could be compared to
experiment, are not specific to Amber, so try a general literature search
to find a publication doing something like what you want; then see if
you can adapt such a method to your needs. To me, this sounds like a
hard problem to do well.

...dac

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