VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Thu Feb 17 2005 - 03:43:21 CST

On Wed, 16 Feb 2005 21:09:12 -0800 Brian Kidd wrote:

brian,

> i'm looking for a way to determine the bond energy (e.g. vdw,
> electrostatic, hbond) between atoms on different residues. ideally,

VMD does not do any (energy) calculations just visualization.
so to determine those values, you either need to dump them
during the simulation of your trajectory or re-evaluate the energies
from an existing trajectory with an MD (like) code (i know that
gromacs supports this, maybe others, too).

of course you need the exact matching potential/force field parameters
and topology files to get the proper values.

> i'd like to set up a loop to be able to determine the bond energies at
> each time step during the simulation (i.e. based off of a dcd file).
> does anyone know of a way to do this in vmd?

if you only want to look at subsystems, you can have VMD write
out a trajectory for those subsystems via the selection commands,
but you still need an (adapted) MD code to calculation the energies.

regards,
        axel.
>
> thanks,
> -brian
> 

--
=======================================================================
Axel Kohlmeyer      e-mail:  axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
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                   http://www.theochem.ruhr-uni-bochum.de
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.