From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Aug 11 2008 - 13:35:11 CDT

On Mon, 11 Aug 2008, Valeria Molinero wrote:

VM> John,
VM>
VM> the new version you compiled seems to produce the right g(r). Thanks!

is it faster, too?
if you have a multi-core cpu it should run multi-threaded now...

VM> May I ask how it is computing the volume that is using to normalize the
VM> g(r)?
VM> I remember there was something fishy with it before and i wonder if this
VM> version fixed it.

this was a different bug (actually two bugs that mostly compensated
each other) that got fixed already a while ago.

cheers,
   axel.

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

-- 
=======================================================================
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.