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On 31/05/2012 7:46 PM, Acoot Brett wrote:
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<div><span>Hi Mark,</span></div>
<div><br>
<span></span></div>
<div><span>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.</span></div>
</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:1338457569.69790.YahooMailNeo@web121805.mail.ne1.yahoo.com"
type="cite">
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255); font-family: times new roman,new york,times,serif;
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<div><br>
<span></span></div>
<div><span>Could you give some further clarification?</span></div>
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<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
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<span></span></div>
<div><span>Cheers,</span></div>
<div><br>
<span></span></div>
<div><span>Acoot<br>
</span></div>
<div><br>
</div>
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<div style="font-family: times new roman,new york,times,serif;
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<div dir="ltr"> <font face="Arial" size="2">
<hr size="1"> <b><span style="font-weight: bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Thursday, 31 May 2012 4:48 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] How GROMACS calculate the energy of
hydrogen bond<br>
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<div> On 31/05/2012 4:42 PM, Acoot Brett wrote:
<blockquote type="cite">
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rgb(255, 255, 255); font-family: times new roman,new
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<div style="margin: 0cm 0cm 10pt;"
class="yiv19733074MsoNormal"><font style=""
face="Calibri">Dear All, </font></div>
<div style="margin: 0cm 0cm 10pt;"
class="yiv19733074MsoNormal"><font style=""
face="Calibri">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?</font></div>
</div>
</blockquote>
<br>
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.<br>
Observables like hydrogen bonds and the hydrophobic
effect arise from them.<br>
<br>
Mark<br>
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