From: John Stone (
Date: Thu Apr 09 2015 - 21:02:03 CDT

  The number of atoms depends on the energy term being measured
(bonds, angles, dihedrals, etc). This was a special feature added
to VMD in support of the older "paratool" force field parameterization
plugin. If you're interested in doing more sophisticated energy evaluations
you may prefer to use namdenergy at present. There may be another way of
computing energies in a future version of VMD depending on how developments

  John Stone

On Thu, Apr 09, 2015 at 03:39:49PM -0700, Gianluca Interlandi wrote:
> Dear list,
> Starting with version 1.9.1 the measure command of VMD can also
> calculate the energy:
> energy energy_term atom_list [parameters] [options]: Returns the
> specified energy term for a given set of atoms. The energy term must
> be one of bond, angle, dihed, imprp, vdw or elect where vdw stands
> for 'van der Waals' and elect for electrostatic energy. The energy
> is computed based on the CHARMM force field functions, the given
> parameters and the current coordinates.
> However, I cannot find an example how to use it. Is "atom_list" just
> two atoms or can it be multiple atoms? Based on the parameters, it
> looks like it calculates the energy between two atoms.
> Thanks,
> Gianluca
> -----------------------------------------------------
> Gianluca Interlandi, PhD
> +1 (206) 685 4435
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

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