From: Valeria Molinero (valeria.molinero_at_utah.edu)
Date: Tue Aug 12 2008 - 18:35:42 CDT

John & Axel,
thanks for your responses.
I do not see it running noticeable faster... but I am running it in a
humble macbook and did not time it.
thanks so much,
vale

On Aug 11, 2008, at 12:35 PM, Axel Kohlmeyer wrote:

> 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.

______________________________

Valeria Molinero
Assistant Professor of Chemistry
University of Utah
315 South 1400 East Rm 2020
Salt Lake City, UT 84112-0850
on campus: 324 INSCC
(801) 585-9618; fax (801)-581-4353
valeria.molinero_at_utah.edu