Re: [AMBER] how to calculate diffusion coefficient ?

From: Daniel Roe <>
Date: Wed, 22 Jan 2014 14:46:31 -0700

Hi, sorry for the delay in replying,

On Tue, Dec 31, 2013 at 8:31 PM, Sohag Biswas <> 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,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jan 22 2014 - 14:00:03 PST
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