Hi,
There's actually a reasonably detailed explanation of how to do this
in the Amber 14 manual using the cpptraj 'diffusion' command (section
28.10.14). You'll probably want to use the 'average' keyword. Good
luck,
-Dan
On Thu, Dec 18, 2014 at 8:28 AM, Robin Jain <robinjain.chem.gmail.com> wrote:
> Dear all,
> I am new comer in Md and i have simulated a organic molecule in 1024
> methanol molecule. After equilibration using NVT ensemble i did 10ns
> production run in NVE ensemble. Now i want to calculate diffusion
> coefficient and plot of MSD. I donot know how to do this. So i request
> you to help me in this regard.
> Thanking You.
> --
> Robin Jain
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Thu Dec 18 2014 - 08:30:02 PST
