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.
Center for Molecular Modeling at
University of Pennsylvania
231 S 34th Street, Philadelphia, PA 19104-6323
On Wed, Mar 11, 2009 at 8:07 AM, Shahid Qamar <qamar13_at_hotmail.com> wrote:
> 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?
> Shahid Qamar
> Windows Live™ Groups: Create an online spot for your favorite groups to
> meet. Check it out.
> Windows Live™: Keep your life in sync. Check it out.
> Express your personality in color! Preview and select themes for Hotmail®.
> See how.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:28 CST