VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 26 2011 - 18:35:47 CST
- Next message: superdirac: "a problem about multiplot"
- Previous message: Narayanan Veeraraghavan: "Question regarding g(r) utility"
- In reply to: Narayanan Veeraraghavan: "Question regarding g(r) utility"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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.
- Next message: superdirac: "a problem about multiplot"
- Previous message: Narayanan Veeraraghavan: "Question regarding g(r) utility"
- In reply to: Narayanan Veeraraghavan: "Question regarding g(r) utility"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]