Hi,
Can you provide some more details about your simulation (# of waters,
input parameters, etc)? Did you perform your simulation in the
microcanonical ensemble? Were your trajectory frames really recorded
every 2 ps? Does the calculated value change if you increase or
decrease the size of the windows?
That being said, 7 isn't too far off from published values which are
around 6 (see e.g. Mark & Nilsson, JPCA 2001, 105, p.9954-9960:
http://pubs.acs.org/doi/abs/10.1021/jp003020w).
-Dan
On Wed, Aug 13, 2014 at 11:09 PM, DEBOSTUTI GHOSHDASTIDAR
<debostutighosh.gmail.com> wrote:
> Dear Amber Users
>
> I am using AmberTools14's diffusion command to calculate the MSD of bulk
> water (TIP3P) for a box of DNA-water simulations. I calculated the MSD for
> five 1-ns windows and get an extremely high *D *of ~7x10^-5 cm2/s whereas
> the value should be around ~2.3x10^-5 cm2/s. The D of TIP3P is known to be
> overestimated but the value I am getting is too high. I use the following
> command:
>
> trajin xmd.crd 2001 2500 1
>
> unwrap :1-8046 //all residues
> center :1-24 mass origin //DNA residue numbers
> image origin center familiar
>
> diffusion 2.0 DNA_water_bulk_win5 :WAT.O average
>
>
> Thanks in advance for any help
>
>
> --
> Debostuti
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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
(801) 585-6208 (Fax)
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Received on Fri Aug 15 2014 - 08:30:02 PDT
