VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Feb 24 2007 - 21:25:14 CST

On Sat, 24 Feb 2007, Jianhui Tian wrote:

JT> Hi all,
JT>
JT> I am using the analysis tool of VMD to do radial distribution function of
JT> Sodium Ions to a charged group of protein. For selection 1, I put the
JT> charged group of the protein and for selection 2 I put the Ions. The g(r) I
JT> got has a peak amplitude of about one hundred and for for the protein
JT> charged group the g(r) didn't go to 1. Does anyone know what exactly the

whether the g(r) goes to 1 for large r depends on the flags you use
and what kind of input you provide and whether your ions are equally
distributed in the 'bulk' of your system w.r.t. to your reference
selection, averaged over the number of frames.

JT> radial distribution analysis do? And how it works? Thanks a lot in advance.

for an explanation of what a g(r) is and how it is computed,
please have a look into the literature referenced in the
plugin documentation at:

http://www.ks.uiuc.edu/Research/vmd/plugins/gofrgui/

cheers,
   axel.

JT>
JT> Jianhui
JT> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.