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

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).

axel.

> Best,
> Mert
>
>  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
> +98.7521
> 1             1             +219.402      +347.777      +184.239
> +16.931       -515.662      -144.068      +768.348      -659.73
> +108.619
> 2             2             +221.796      +331.97       +187.3
> +23.1723      -521.071      -155.589      +764.237      -676.659
> +87.5782
>

-- 
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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