From: Axel Kohlmeyer (
Date: Tue Jun 05 2007 - 19:41:24 CDT

On Tue, 5 Jun 2007, Arneh Babakhani wrote:

AB> Hi,
AB> Is there a way to measure hbonds between selections that are from
AB> different molecules? I ask, b/c I noticed that in the manual, it states
AB> that to use 'measure hbonds', selections must be from the same molecule.

it is in the manual, because this is how it is implemented.

however, molecule is to be understood in the VMD sense of a molecule,
i.e. the coordinates have to be read from the same file. which is
not the same molecule in the chemical sense.

if you have two different VMD molecules (i.e. want to compare hydrogen
bonds between two different files), you'll have to merge the files and
read the resulting file into VMD.

hope that clarifies it.


AB> Thanks,

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.