Re: [AMBER] msd calculation using ptraj diffusion

From: Monika Sharma <mondyn.gmail.com>
Date: Sat, 27 Feb 2010 15:00:09 +0530

Hello,

Thank you replying. I agree with you. Then how is it possible to get
diffusion coefficient values of individual ions from such simulation data.
Any other reasonable way?

Regards
Monika

On Sat, Feb 27, 2010 at 2:52 PM, <hannes.loeffler.stfc.ac.uk> wrote:

> > But msds of the atoms of interest (no doubt in increasing
> > order) are spiky, irregular, with very small linear behavior inbetween.
>
> Yes, that's to be expected. That simply shows the random movements of
> individual particles. Only when you average over a large numbder of
> particles will you get a more linear behaviour. It will also make a
> difference whether your ions move in a homogeneous environment or not.
>
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-- 
((¯`·_.·[Monika]·._·´¯))
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Received on Sat Feb 27 2010 - 02:00:03 PST
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