Re: What is the Potential Energy of a Protein in Namdenergy

From: Mert Gr (
Date: Tue Mar 16 2010 - 07:59:31 CDT

Thanks a lot to both of you. Now its clear to me. I thought that the energy
reference is assumed to be zero at the bottom of the potential well. I
should take a better look into the user guide.

. What state do
> you define as having zero energy? NAMD does not approach this question
> the way you do in your harmonic approximation.
> Best,
> Jerome
> On 16 March 2010 11:51, Mert Gr <> wrote:
> > Dear all,
> > Lets say that I have an harmonic system consisting of N atoms. Then my
> > potential energy should be 3NkT.
> > However due to unharmonicity in a real system the energies should deviate
> > from this value.
> > When I ask Namd to evaluate just the energy of the protein via
> Namdenergy,
> > it gives me conformational energy, non-bonded energy and a total energy--00163683395895a7620481ea9134--

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