From: Axel Kohlmeyer (
Date: Wed Oct 11 2006 - 14:46:15 CDT

On Wed, 11 Oct 2006, Arturas Ziemys wrote:

AZ> Hi,

AZ> I realized that gofr in VMD does not count for volume corection, if
AZ> there is, say, water (OH2) distribution around the protein case. Is
AZ> it ?

the way it is programmed and run, measure gofr can only
correct for double counting (i.e. if you have a bulk
water system with 200 water molecules, the limit
for g(r->oo) will be 1.0 and not 199/200. other than
that there is no easy way to program 'knowledge'
about your structure into the code.

i recommend you have a look at the source code
to be sure of it.

feel free for submit suggestions/changes to improve on it.


AZ> With best
AZ> Arturas

Axel Kohlmeyer
   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.