VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Sep 07 2011 - 06:18:06 CDT

Hi Manish,

how about this:
puts [[atomselect top "name OH2 and x>-5 and x<5 and y>-5 and y<5 and
z>-5 and z<5"] num]

Cheers,
Jerome

On 6 September 2011 18:11, Manish <manish.datt_at_hotmail.com> wrote:
> Hi All,
>
>
>
> Is there a way to calculate water molecules inside a box of specified
> dimensions using VMD. For instance, I’ve my protein centered on origin and
> would like to calculate water molecules inside a box that is also centered
> on origin. Basically, I’m trying to calculate water molecules inside the
> protein and instead of calculating waters within certain distance cutoff
> around the protein, I would like to count waters with a box (of different
> sizes). Any help in this regard would be greatly appreciated.
>
>
>
> Regards,
>
>
>
> Manish
>
>