<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><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><br><span></span></div><div><span>Could you give some further clarification?</span></div><div><br><span></span></div><div><span>Cheers,</span></div><div><br><span></span></div><div><span>Acoot<br></span></div><div><br></div>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <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> </font> </div> <br><meta http-equiv="x-dns-prefetch-control" content="off"><div id="yiv19733074">
<div>
On 31/05/2012 4:42 PM, Acoot Brett wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;">
<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>
</div>
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