[gmx-users] How GROMACS calculate the energy of hydrogen bond
acootbrett at yahoo.com
Thu May 31 11:46:09 CEST 2012
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?
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at 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:
>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
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