From: Axel Kohlmeyer (
Date: Mon Jan 12 2009 - 14:37:05 CST

On Mon, 12 Jan 2009, Alison Grinthal wrote:

AG> Hi - Sorry if this exists and I just didn't find it, but is there any VMD
AG> plugin that finds the centers of mass for separate groups of residues in a
AG> molecule and then calculates the distances between them? Many thanks.


you can implement this as a custom script very easily.
here is some kind of template (untested, so beware of typos):

set sel1 [atomselect top "<selection text for group 1>"
set sel2 [atomselect top "<selection text for group 2>"

set len [vecdist [measure center $sel1 weight mass] \
                 [measure center $sel2 weight mass] ]



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.