From: Axel Kohlmeyer (
Date: Thu Feb 26 2004 - 03:46:52 CST

On Wed, 25 Feb 2004 10:31:45 -0800 (PST) Sichun Yang wrote:

> Dear VMD users,
> I have a question on the hydrogenbond energy.
> How can I calculate it for one specific NH-CO pair along a long trajectory
> using VMD (Tkcon, command ...)?

hello sichun,

short answer: you cannot.
to explain: VMD does not know, which potentials
you have used. one thing that you can do is to extract the
relevant coordinates (using atomselect), write them to a file
and then write a short program to evaluate them from the
force-field parameters, you have used in your simulation.

        axel kohlmeyer.

> Thanks,
> Sichun

Axel Kohlmeyer      e-mail:
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum         
If you make something idiot-proof, the universe creates a better idiot.