From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 16 2010 - 06:55:55 CDT
On Tue, Mar 16, 2010 at 5:51 AM, 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.
why so? have you considered the fact, that the energy
in the minimum of the non-bonded potential is negative?
granted it is not a good approximation, but saying "far
away" does not describe it well, either.
> So when I am refering to the potential energy of the protein only, am I
> refering to the conformational energy?
no. all of it. remember, that absolute energies are meaningless,
only energy differences between two conformations using the
same model (=force field or parameter set).
> 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
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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