[AMBER] Calculating diffusion Constant D

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Thu, 25 Jul 2013 11:07:19 +0100 (BST)

Dear amber experts,

I need some clarification on calculating the diffusion constant D from MD simulation for bilayer system using  "diffusion" command in ptraj.

The command I used is : 
"diffusion :1-1 5.0 average diffusion-malto-thermo1.dat"

I get to see information saying that 
      Only the average results will be dumped to diffusion-malto-thermo63.dat_?.xmgr
      The time between frames in psec is 5.000.
      To calculated diffusion constants, calculate the slope of the lines(s)
      and multiply by 10.0/6.0; this will give units of 1x10**-5 cm**2/s
      The atoms in the calculation follow: :63"

I get five files. I choose the file with  *z extention to calculate the gradient. 

For this I used gnuplot with command below:
" f(x) = b + m*x "
" fit f(x) "allxy-mal-cel-iso-bcm-diffusion_z.dat" using 1:2  via b,m "

I get values for "b" and "m" as below:
=======================            ==========================

b               = 1.12224          +/- 0.003892     (0.3468%)

m               = 0.0337373        +/- 0.0001686    (0.4997%)

This means I get the gradient value as "0.0337373" and the y-intercept as "1.12224".

For now I want to calculate the diffusion.
 So I times 0.0337373 with  (10/4) since mine is bilayer (2 dimensional system).
I get "0.08434325". 

Finally should I write my answer as

0.08434325 x 10^(-5) cm^2/s

Is this is the correct way of interpret the D value?

I appreciate anyone's reply to this post.

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
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Received on Thu Jul 25 2013 - 03:30:02 PDT
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