[gmx-users] How GROMACS calculate the energy of hydrogen bond

[Mark Abraham]

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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