Re: FW: Water density of water Box

From: Grace Brannigan (gracebrannigan_at_gmail.com)
Date: Wed Mar 11 2009 - 09:26:08 CDT

Hi Shahid,

Are you using vmd with perspective projection rather than orthographic
(under display)? That will make the edges of a water box look less dense.
If so, try switching to orthographic and you'll be able to see that its
actually a constant density.

-Grace

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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