VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jul 22 2008 - 19:09:09 CDT

On Tue, 22 Jul 2008, Valeria Molinero wrote:

VM> Axel,
VM>
VM> where i can get the version you mention? I am using version 1.8.6 for mac
VM> intel.

please see http://www.ks.uiuc.edu/Reasearch/vmd/alpha/
it's been posted on and off here and also linked from
the vmd homepage (somewhere under development).

VM> The bin size I use is 0.1A. In the version I have I must use a small
VM> bin because the volume used in the normalization is not the one of a
VM> sphere shell but its limiting value 4 pi r^2 binsize. Is this what
VM> you fixed?

there were three issues that (mostly) compensated each other.
the value of r for each bin, how borderline cases were sorted
in and how the very first bin was placed and normalized.

cheers,
   axel.

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