Hi Daniel
I have 8000 water in the system run in NPT at 298K and 1atm pressure.
Trajectories were recorded every 2ps. I tried with a single window and 5
windows...both gave be approximately same readings.
Thanks
On Fri, Aug 15, 2014 at 8:37 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debostuti Ghosh Dastidar
PhD Scholar
Indian Institute of Technology Madras
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Received on Fri Aug 15 2014 - 10:00:02 PDT
