Hi Daniel
My value is 0.027x10^-9 m2/s which is essentially same as 0.027x10-5
cm^2/s, which is low for water
Thanks
On Fri, Mar 15, 2013 at 8:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > 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 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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>
--
Debostuti Ghosh Dastidar
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Received on Fri Mar 15 2013 - 23:00:02 PDT
