Dear Amber user,
Now, I'm trying to calculate the diffusion coefficient using MSD graph which
was made by PTRAJ "diffusion". I know (Slope)*(10/6) is the way of
calculating diffusion coefficient from MSD graph. But I don't know exact
unit of this value. Which one is correct unit? Just Cm^2/Sec or
10^(-5)*Cm^2/sec?(I read some previous messages regarding this question, but
someone replied Cm^2/Sec, another replied 10^(-5)*Cm^2/sec)
And I have one more question, I've got 2 trajectories regarding production
MD which has periodic boundary. Unwrapped and wrapped(centered).
Which one is the best file to use as calculating the diffusion coefficient?
I appreciate it a lot if you reply in detail !
Thanks in advance.
Hoshin Kim.
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Hoshin Kim
Now)
Visiting Scholar
Department of Chemical and Biomolecular Engineering
North Carolina State University
Raleigh, NC 27695
Phone: 919-986-9258
Also)
Graduate student (M.D. candidate)
Ionic Liquids Team(ILs) in Bio Nano Process Lab
Department of Biological Engineering,
2S 113, Engineering building Inha University,
253 Yonghyeon Dong, Nam Ku
Incheon, KOREA
TEL) +82-32-860-8655
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Received on Tue Aug 17 2010 - 14:00:03 PDT
