From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Mar 11 2009 - 10:24:00 CDT
Hi Shahid,
is your concern about the initial conformation of a system or what it
does after some simultion?
Have you run any equilibration with constant pressure? You probably
don't have enough water for the size of your box...
Peter
Shahid Qamar 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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