Hi Mark,
It is confusing. As you know, for the same hydrogen bond in a protein, the
related hydrogen bond angle and bond length can vary within a scope during the
whole simulation process, however this small vibration of the hydrogen bond
angle and length can lead to significant energy change, and correspondingly the
energy of a hydrogen bond in simulation can be varied significantly. In
comparison with hydrophobic effect, it would be too much is the energy of the
hydrogen bond would be not calculated continuously.
Could you give some further clarification?
Cheers,
Acoot
________________________________
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Thursday, 31 May 2012 4:48 PM
Subject: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond
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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