Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface

From: Jim Phillips (
Date: Thu Oct 24 2013 - 10:01:30 CDT

On Thu, 24 Oct 2013, Norman Geist wrote:

> I'm currently adapting some of the replica.namd TCL code. I noticed, that
> the energies got through save_array output different values before and after
> outputenergies took effect. Could it be that namd stores these values in a
> different unit and that the energies get transformed before printed to the
> log? What's the exact factor here?

Energy is always kcal/mol. The outputEnergies setting also controls how
often nonbonded (vdw and electrostatic) energies are calculated, so you
want outputEnergies to be a multiple of fullElectFrequency and
steps_per_run to be a multiple of outputEnergies.

Beyond that I don't understand your question.

> Additionally, the procedure how to get these energy values isn't documented
> very well. Are these values accessible from TCLforces, too, this would save
> me from doing "run 1" what unfortunately comes with "stepspercycle 1"
> "fullelectfrequency 1" and "nonbondedfreq 1".

Try "run 0" instead. It'll do one energy evaluation with no integration.

We could make energies from the *previous* timestep available in tclForces
(the way total forces on requested atoms are available now). This would
provide the timestep synchronization that I think you're looking for.


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