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On 31/05/2012 4:42 PM, Acoot Brett wrote:
<blockquote
cite="mid:1338446574.88348.YahooMailNeo@web121806.mail.ne1.yahoo.com"
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<div style="MARGIN: 0cm 0cm 10pt; RIGHT: auto" class="MsoNormal"><font
style="RIGHT: auto" face="Calibri">Dear All,
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<div style="margin: 0cm 0cm 10pt; right: auto;"
class="MsoNormal"><font style="right: auto;" 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>
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<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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