RE: [AMBER] msd calculation using ptraj diffusion

From: <hannes.loeffler.stfc.ac.uk>
Date: Sat, 27 Feb 2010 09:22:20 -0000

> 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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Received on Sat Feb 27 2010 - 01:30:03 PST
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