Hi, sorry for the delay in replying,
On Tue, Dec 31, 2013 at 8:31 PM, Sohag Biswas <cy13p1001.iith.ac.in> wrote:
> After getting MSD plot, to calculate diffusion coefficient, I
> multiplied the slope by 10/6, which is given in Amber 13 tools. Now when i
> am changing time-step, my diffusion coefficient value also changes. I
> started calculation MSD by taking time-step 20 (*dt*ntwx*) to 1. So, I want
> to know that how to choose time-step and what will be unit?
>
As you stated above, given that your time step is 2 fs and you are writing
every 10000 steps the time between frames (i.e. your trajectory time step)
is 20 ps. As stated in the manual, <time_per_frame> is expected in ps; the
value of 10.0/6.0 can only be used to convert units of Angstrom^2/ps (the
slope of the lines from your MSD plots) to 1x10^-5 cm^2/s. The reason your
diffusion coefficient value changes when you change the time step is
because the diffusion coefficient itself is related to time.
Hope this helps,
-Dan
--
-------------------------
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 Jan 22 2014 - 14:00:03 PST
