VMD-L Mailing List

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Mon Oct 25 2010 - 11:44:58 CDT

On Mon, Oct 25, 2010 at 10:21 AM, sarah k <dailycolors_at_gmail.com> wrote:

> Dear VMD users,
>
> My problem is putting CNT(8,2) in water and running it for g(r)
> calculation.
> in RDF window I actually don't know what I should do.
> I am confused. in selection 1: what I must type exactly?(what word?)? What
> about selection 2?
>
> or in the histogram parameters?
> Thanks for your guide and attention!
>
> Cheers,
> Sarah K.
>
> Dear Sarah,

> RDF is the probability of finding selection 1 at a distance r of selection
> 2. 'max r' is the maximum cut off distance within which you calculate this
> probablility.

> You can put the selection word as you would in the VMD graphical
> representation. For instance, if you want to look at the distribution of
> Oxygens in water box, you can define as "name OH2" in both selection 1 and
> 2.
>

Hope is clear.
Ramya
TCBG, UIUC