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
"DIFFUSION
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,
Malaysia
vjramana.gmail.com
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Received on Thu Jul 25 2013 - 03:30:02 PDT
