Hi,
Maybe there is a unit conversion issue? You don't say what units
you're comparing to, but I believe the units you will get from
analyzing the output of cpptraj/ptraj diffusion (i.e. slope_of_line *
(10/6)) is 1E-5 cm^2/s.
-Dan
On Fri, Mar 15, 2013 at 4:32 AM, DEBOSTUTI GHOSHDASTIDAR
<debostutighosh.gmail.com> wrote:
> Dear Amber users,
>
> I have a system comprising of dna dodecamer in a box of water (8000 water
> molecules). When I calculate the diffusion coefficient of water in this
> system, I get a value of 0.027x10^-9, which is two orders of magnitude
> slower than the experimental value. I directly plotted the data of
> water_a.xmgr output, calculated the slope and multiplied by 10/6. Am I
> missing something here.
>
> Thanks in advance for any suggestions.
>
> --
> Debostuti Ghosh Dastidar
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--
-------------------------
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 Fri Mar 15 2013 - 08:30:03 PDT
