Hi,
On Mon, Oct 15, 2012 at 5:56 AM, Alan <bl1bl2bl3bl4.sina.com> 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
cm^2/s.
-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) 585-9119 (Fax)
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Received on Mon Oct 15 2012 - 14:30:03 PDT
