VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 01 2013 - 09:25:13 CST

Hi,
  The values should be in absolute distance, but in Angstroms, not nm.
Another thing to be aware of is that you may need to use your own custom
normalization if you're dealing with membranes, as the built-in
normalization computes a straightforward histogram bin shell
volume normalization and doesn't try to handle water, membrane, or
protein specially.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 01, 2013 at 04:05:58AM -0500, Bharath K. Srikanth wrote:
> Hi all,
>
> I'm trying to calculate the radial pair distribution function of a protein
> with respect to a lipid bilayer. Could you please inform me whether the
> values on the x-axis (of the graph obtained from the vmd script gofr) are
> absolute distance (in nm), or some other form of normalized distance? If
> it is absolute distance, I need to try again, because my graph's values
> are incorrect.
>
> Sincerely
>
> --
> Bharath K Srikanth
> IV Year B.Tech
> Dept. of Chemical Engineering
> Indian Institute of Technology, Guwahati
> Ph: (+91) 88762 03224
> E.mail: s.bharath_at_iitg.ernet.in 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078