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

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 31 11:54:04 CEST 2012

On 31/05/2012 7:46 PM, Acoot Brett wrote:
> 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.

It isn't, if the model physics isn't paramtrized to include it 
explicitly - which is the case for all the force fields in GROMACS.

> Could you give some further clarification?

What are trying to do? Measuring "the strength of a hydrogen bond" 
requires you identify a state with and without it and a path between 
them over which you can integrate.


> Cheers,
> Acoot
> ------------------------------------------------------------------------
> *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:
>> 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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