From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Mar 11 2009 - 10:30:05 CDT
Most likely, because when you solvate, several water molecules are
deleted if they overlap the box edges too much (which would cause them
to clash with molecules on the other side of the periodic box). When
you're at the corners, this happens along three different edges, and
you get a lot of deletions: at the center of a box face, or in the
middle of the box, it happens much less, or never.
Giacomo
---- -----
Giacomo Fiorin
Center for Molecular Modeling at
University of Pennsylvania
231 S 34th Street, Philadelphia, PA 19104-6323
phone: (+1)-215-573-4773
fax: (+1)-215-573-6233
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mail: giacomo.fiorin_<at>_gmail.com
web: http://www.cmm.upenn.edu/
---- ----
On Wed, Mar 11, 2009 at 8:07 AM, Shahid Qamar <qamar13_at_hotmail.com> wrote:
>
>
>
>
>
>
>
> Hi,
> I have a 15 base ssDNA molecule and when I solvate it in a waterbox, the
> density of water if not constant at the six edges of the box. The density
> looks uniform at the center but it reduces at the corners. Any idea why it
> is like that?
>
> Thanks
> Shahid Qamar
>
>
>
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