Hi,
Just to make Jason's answer explicit, for a diffusion calculation
*don't* use imaging/centering or anything else that may mess with the
relative positions of molecules. *Do* use 'unwrap' prior to the
'diffusion' command to ensure the molecules take continuous paths.
-Dan
On Fri, Jan 23, 2015 at 1:02 AM, Robin Jain <robinjain.chem.gmail.com> wrote:
> Dear all,
> As a test run, we are trying to compute diffusion constant of water.
> We have taken 64 water molecules. I am confused about the "center" and
> "image" command. Using the following command, we are getting the value
> 2.918 and without using the two commands we are getting a different
> value (2.026). kindly suggest.
>
> trajin X.mdcrd 1 last 1
> unwrap :1-64
> center :1-64 mass origin
> image origin center familiar
> diffusion 0.25 diff.out :1-64 average
> go
>
> --
> Robin Jain
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Fri Jan 23 2015 - 10:00:03 PST
