Re: using namd to compute energies

From: Shirley Hui (
Date: Tue Feb 15 2005 - 14:24:46 CST

I don't know if this will do what you want, but you can use mdenergy to
calculate energies of structures in DCD. I don't know if you can compute the
energy of just the ligand with one amino acid though - I've never used it in
that way before. I think the tool can be used from VMD as well.
The energy calculation is the same as what NAMDs uses to compute energies
(minus rounding errors).

----- Original Message -----
From: "Leandro Martinez" <>
To: <>
Sent: Tuesday, February 15, 2005 2:24 PM
Subject: namd-l: using namd to compute energies

> I ran a simulation with namd and now I got my dcd file with
> the trajectory. The system is composed of a protein and a ligand.
> Now, I would like to compute the interaction energy (vdw+electrostatic) of
> the ligand with one of the amino acids of the protein, at every step
> of my dcd file. Is there any simple way to use namd for performing
> this task? Could a tcl script do that either on namd or vmd? VMD
> is able to read the force field?
> Thanks in advance,
> Leandro Martinez.
> ----------------------------------
> Leandro Martinez
> Department of Physical Chemistry
> Institute of Chemistry
> State University of Campinas
> ----------------------------------

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