[gmx-users] Coul-14 + dihedral + torsion

Samuel Flores samuel.flores at yale.edu
Fri Mar 25 23:18:09 CET 2005

Howdy all,

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
enlighten me?

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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