What is the Potential Energy of a Protein in Namdenergy

From: Mert Gür (gurmert_at_gmail.com)
Date: Tue Mar 16 2010 - 05:51:39 CDT

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?
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

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