VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 11 2008 - 11:45:07 CDT

Hi,
  Nothing has changed in regards to how the histogram is normalized,
but a bug was fixed that was causing a floating point number to be
inadvertently truncated to an integer.

Cheers,
  John

On Mon, Aug 11, 2008 at 10:40:45AM -0600, Valeria Molinero wrote:
> John,
>
> the new version you compiled seems to produce the right g(r). Thanks!
>
> May I ask how it is computing the volume that is using to normalize
> the g(r)?
> I remember there was something fishy with it before and i wonder if this
> version fixed it.
>
> thanks you very much for your help,
> vale
>
>
> On Aug 6, 2008, at 10:24 AM, John Stone wrote:
>
> >Valeria,
> > I've posted the new test build on the VMD Public project on
> >BioCoRE. Please try it out and let us know if this solves
> >the problem you had been having. If you haven't downloaded test
> >builds before, please see this page:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Sun, Aug 03, 2008 at 06:00:27PM -0600, Valeria Molinero wrote:
> >>John,
> >>thanks so much. I am looking forward to it.
> >>cheers,
> >>vale
> >>
> >>On Jul 31, 2008, at 12:00 PM, John Stone wrote:
> >>
> >>>
> >>>I should have a new test build containing Axel's patch available
> >>>pretty shortly. I'll let you know when it's posted.
> >>>
> >>>Cheers,
> >>>John Stone
> >>>vmd_at_ks.uiuc.edu
> >>>
> >>>On Tue, Jul 22, 2008 at 05:58:25PM -0600, Valeria Molinero wrote:
> >>>>Axel,
> >>>>
> >>>>where i can get the version you mention? I am using version 1.8.6
> >>>>for
> >>>>mac intel.
> >>>>
> >>>>The bin size I use is 0.1A. In the version I have I must use a
> >>>>small
> >>>>bin because
> >>>>the volume used in the normalization is not the one of a sphere
> >>>>shell
> >>>>but its
> >>>>limiting value 4 pi r^2 binsize. Is this what you fixed?
> >>>>
> >>>>thanks for your help,
> >>>>vale
> >>>>
> >>>>On Jul 22, 2008, at 4:06 PM, Axel Kohlmeyer wrote:
> >>>>
> >>>>>if you download a recent alpha test version for the next VMD
> >>>>>release, gofr calculations should work fine.
> >>>>
> >>>>______________________________
> >>>> 

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