[AMBER] question on diffusion coefficient calculation using ptraj

From: Ganesh Kamath <gkamath9173.gmail.com>
Date: Fri, 21 Jan 2011 10:19:16 -0500

Hi Amber Folks,
   I am computing the self diffusion coefficent of box of SO2 molecules. I
ptraj facility to compute the diffusion coefficient.
trajin md1.crd
diffusion :1-500 1.0 average diffusion

I get 5 xmgr files diffusion_x.xmgr, diffusion_y.xmgr, diffusion_z.xmgr,
diffusion_r.xmgr and diffusion_a.xmgr

Which file of diffusion_r.xmgr and diffusion_a.xmgr should I use to compute
the slope and multiply by 10/6.

If anyone could please help me resolve this it would be grateful.

thanks for your time.

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Received on Fri Jan 21 2011 - 07:30:09 PST
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