From: Manish (
Date: Wed Sep 07 2011 - 09:19:55 CDT

Hi Jerome,

Thanks! That`s exactly what I was looking for.



-----Original Message-----
From: [] On Behalf Of Jérôme Hénin
Sent: Wednesday, September 07, 2011 7:18 AM
To: Manish
Subject: Re: vmd-l: Count waters inside a specified box

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]


On 6 September 2011 18:11, Manish <> 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