VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 26 2011 - 18:35:47 CST

On Wed, Jan 26, 2011 at 6:30 PM, Narayanan Veeraraghavan
<narayanan.veeraraghavan_at_gmail.com> wrote:
> Hi,
> I am using the g(r) gui to calculate the g(r) of solvent metal ions, say,
> Na+ around three specific atoms of my protein (different atom types,
> belonging to different residues but close to each other in space).
>
> Now, my question is, how is the r determined? Is it from the *geometric
> center* of three atoms? Or, does it select all Na+ atoms within r of

no.

> *atleast one* of the three atoms? Or does the function do some kind of

no.

> averaging of the g(r) from each of these three atoms? Would appreciate
> specific pointers.

the last option is what happens. r is computed, histogrammed and
normalized for each permutation of 1 atom in selection 1 with one
atom of selection 2.

it is an "atomistic" g(r). anything more sophisticated would be _very_
case specific and VMD usually does not have the information necessary
for it, so measure gofr doesn't even try.

cheers,
    axel.

>
> Details:
> selection1: index 10 35 1090
> selection 2: resname NA
> Assume some values for delta and max r.
>
> Thanks,
> Narayanan
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.