VMD-L Mailing List

From: Albert (mailmd2011_at_gmail.com)
Date: Thu Jun 28 2012 - 07:18:11 CDT

yes, it would be very nice if Fariba can talk a little bit more on such
scripts.

thank you very much
Albert

On 06/28/2012 12:38 PM, meisam valizadeh kiamahalleh wrote:
> Dear Fariba
> Glad to hear your helpful reply on this matter. May I know if you have
> any TCl script for calculating the water molecule's number over the
> simulation time and a distance from the surface? I guess the
> suggestion that you made here is for finding the number of water
> molecule at a specific time, if I am not mistaken.
> I would be very grateful if you could share your experience with us.
> Cheers,
> Meisam
>
> On Thu, Jun 28, 2012 at 3:39 PM, fariba taghavi
> <faribataghavifariba_at_gmail.com <mailto:faribataghavifariba_at_gmail.com>>
> wrote:
>
> Dear Albert,
> Actually you can not find this option directly in the VMD but, you can
> use TLC to write a short code. My suggestion is to select oxygen atom
> in the hole (for example by "atomselect" to choose oxygen atoms with
> x^2+y^2+Z^2<=16, it is related to the shape of the hole) and then you
> can get the number of your selected atoms.
>
> Good Luck,
> Fariba Taghavi
> PhD Candidate in Physical Chemistry
> Tarbiat Modares University
>
> On 6/27/12, Albert <mailmd2011_at_gmail.com
> <mailto:mailmd2011_at_gmail.com>> wrote:
> > hello:
> >
> > I've finished a MD and I would like to to make statistics
> for the
> > water density in the 'hole' within the protein at specific
> region. I am
> > wondering, is it possible for VMD to do so ? Does anybody have any
> > suggestions? I've searched in the mailist and VMD
> plug-in/scripts pages,
> > but didn't find anything related.
> >
> > thank you very much
> > Albert
> >
>
>