VMD-L Mailing List

From: Manish (manish.datt_at_hotmail.com)
Date: Wed Sep 07 2011 - 09:19:55 CDT

Hi Jerome,

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

Regards,

Manish

-----Original Message-----
From: heninj_at_gmail.com [mailto:heninj_at_gmail.com] On Behalf Of Jérôme Hénin
Sent: Wednesday, September 07, 2011 7:18 AM
To: Manish
Cc: vmd-l_at_ks.uiuc.edu
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]

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
>
>