[gmx-users] Calculate a single hydrogen bond energy in the polypeptide molecule

Sekwan Oh ohsk75 at stanford.edu
Tue Aug 10 09:57:21 CEST 2004

Dear gmx-users,

I'm wondering if we can obtain hydrogen bond energy (e.g. N-H ----- O=C) in 
the polypeptide molecule (which is defined as 1 group of residues e.g LYSH).
I think I can get the bonded and nonbonded energy of the 1 residue of the 
polypeptide (by using g_energy and setting up 'energygrp' command in .mdp file)
, however I haven't found out a way to get the energy between atoms which 
belong to same group of residues.

Thanks :)

Best regards,


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