[gmx-users] Coul-14 + dihedral + torsion
samuel.flores at yale.edu
Fri Mar 25 23:18:09 CET 2005
Many thanks for help given in the past.
I'm currently doing md of a protein in a water box. I'd like to know the
potential and kinetic energies of the protein alone, the potential energy of
the protein-water interaction. It's my understanding that the g_energy term
Coul-LR:Protein-Protein doesn't exist, because it's included in
Coul-SR:Protein-Protein for a groupwise energy analysis. So I am to sum
Coul-SR to Coul-14. But I can't for the life of me find out what exactly
Coul-14 represents, and why it would not be included in Coul-SR. Can anyone
Also, I would think it would be necessary to include energies due to
Dihedral bending and Torsion angle twisting in the protein. But, those
energies are not separated into groups! Am I to assume that all the bending
energy is due to the protein? That doesn't seem right -- surely the water
is responsible for some of that. Also, I don't see a Torsion angle term at
all, even for the system as a whole -- where is this energy?
Thanks in advance for any help you can give.
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