[AMBER] Query regarding the internal energy of protein.

From: Leena Aggarwal <leena.hrc.gmail.com>
Date: Mon, 17 Dec 2018 15:39:29 +0530

Dear Amber Users

I have run the explicit water MD simulation of a protein. I want to
calculate the internal energy of protein from the total energy of the
system which is given as:

Total energy = configurational energy of protein+ protein-solvent
interaction energy + solvent-solvent interaction energy.

Total energy=Ebond + Eangle + Edihedral + E1-4NB + E1-4EEL + EVDWAALS+ EElec

I have got the total energy of the system at each step from the output
files generated during the simulation. In this, the last two terms i.e
Lennard Jones and Electrostatic interaction terms include contributions
from solute-solvent and solvent-solvent interaction energy also.

Any suggestions for calculating the configurational energy of protein from
total energy of the system.
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Received on Mon Dec 17 2018 - 02:30:02 PST
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