Hi,
I suggest looking at the documentation for the 'rotdif' command in cpptraj
for rotational diffusion, and the 'diffusion'/'stfcdiffusion' commands in
cpptraj for calculating self-diffusion.
Hope this helps,
-Dan
On Mon, Feb 24, 2014 at 2:11 AM, Robin Jain <robinjain.chem.gmail.com>wrote:
> Dear all amber users,
> I am doing MD of a organic molecule in methanol and i have a 10 ns
> trajectory file. Now i want to calculate rotational reorientation time (ps)
> and translational diffusion coefficient for that organic molecule. Please
> help me in this regard.
>
>
> --
> Robin Jain
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 26 2014 - 07:30:03 PST
