On 31/05/2012 4:42 PM, Acoot Brett wrote:
Dear All,
The value of the energy of the hydrogen bond has relation with
distance and angle of the hydrogen bond related atoms. As for in the
simulation process, the distance and angle of the hydrogen bond
related atoms may change continuously. Will you please let me know
based on which formula GROMACS calculated the value of the energy of
the hydrogen bonds?
There is no such formula used in MD force fields implemented in GROMACS.
The only non-bonded interactions are the ones you already know about:
electrostatics and VDW.
Observables like hydrogen bonds and the hydrophobic effect arise from them.
Mark
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