From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Mar 16 2010 - 07:10:00 CDT
You are forgetting a major point: the energy reference. What state do
you define as having zero energy? NAMD does not approach this question
the way you do in your harmonic approximation.
On 16 March 2010 11:51, Mert Gür <gurmert_at_gmail.com> 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.
> The conformational energy is in a close vicinity of the harmonic
> approximation. non-bonded has negative sign and tehrefore total energy is
> far away from teh harmonic approximation.
> So when I am refering to the potential energy of the protein only, am I
> refering to the conformational energy?
> Time Bond Angle Dihed Impr
> Elec VdW Conf Nonbond Total
> 0 0 +228.739 +329.297 +186.211
> +22.479 -527.698 -140.276 +766.726 -667.974
> 1 1 +219.402 +347.777 +184.239
> +16.931 -515.662 -144.068 +768.348 -659.73
> 2 2 +221.796 +331.97 +187.3
> +23.1723 -521.071 -155.589 +764.237 -676.659
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