Re: using namd to compute energies

From: Jan Saam (
Date: Thu Feb 17 2005 - 15:44:57 CST

Dear Leandro,

Shirley is right. You can do that with MDEnergy.
Documentation is included in the package.

Regards, Jan

> 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).
> shirley
> ----- 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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