[gmx-users] Potential energy contributions and total pot ener

[Mark Abraham]

pascal.baillod at epfl.ch wrote:
> Dear community,
> 
> I am trying to figure out how potential energy contributions sum up to the total
> potential energy. With g_energy, I can get the following energy contributions of
> my solvated protein system:
> 
> a) protein-protein
> b) protein-solvent
> c) solvent-solvent
> 
> I have two questions:
> 
> 1) I guess the total potential energy would be 
> Etot = a + 0.5*b + c
> 
> 2) Would there be an additional term coming from water molecule bonded energy
> terms? If I call this term d, is there a way to get it? I would finally have:
> 
> Etot = a + 0.5*b + c + d
> 
> Thank you very much for any info!!

All of the terms in the log file and/or g_energy output that are 
energies and are not kinetic or total energies must contribute to the 
potential energy. There aren't any other sorts of energies! So all of 
the bonded, angle, dihedral, improper, restraint, etc. terms must 
contribute.

Mark