Re: [AMBER] How dose ptraj calculate diffusion

From: Daniel Roe <>
Date: Mon, 15 Oct 2012 15:23:57 -0600


On Mon, Oct 15, 2012 at 5:56 AM, Alan <> wrote:
> It doesn't seem like ptraj uses the formula lim <[r(
> t)-r(0)]^2>/6t. So I want to know more about the algorithm ptraj uses.

Correct - ptraj just calculates the raw total distance travelled, as
well as the distances travelled in the X, Y, Z directions. As printed
in the ptraj output, to calculate diffusion constants calc the slope
of the lines and multiply by 10 / 6, which will give units of 1E-5


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) 585-9119 (Fax)
AMBER mailing list
Received on Mon Oct 15 2012 - 14:30:03 PDT
Custom Search