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<p class=MsoNormal><span style='color:#1F497D'>Hi again,<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Yes, you can simply specify sigma
and epsilon, but indeed in your case you do not want to do so but rather to
specify C_6 and C_{12} with the former being zero to avoid attraction.<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Your .top file should include a
[ defaults ] section, perhaps through an #include of a .itp file. Perhaps yours
is in ffamber99.itp (I don’t have it installed so I can’t tell). In
this section there are 5 parameters; the second is a “combination rule”
which must equal 1 for the two numbers to represent indeed C_6 and C_{12} (see
table 5.3, eq. 5.1-5.4, and in page 112).<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>In short, check whether the
second parameter in the [ defaults ] section of ffamber99.itp is 1, if not that’s
probably the problem. Of course, if you change this you’ll screw up all
the other parameters, so it seems you could either change the force field or
create your copy of the files with all the relevant LJ parameters changed to
the “combination rule”=1 convention.<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Ehud Schreiber <br>
<b>Sent:</b> Wednesday, July 28, 2010 3:01 PM<br>
<b>To:</b> 'gmx-users@gromacs.org'<br>
<b>Subject:</b> RE: [nonbond_params] section , choice of parameters<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Amir,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Are you sure you’re giving the parameters indeed as
C_6 and C_{12}? <o:p></o:p></p>
<p class=MsoNormal>According to the combination rule in the [ defaults ]
section, you may be giving the two parameters directly as sigma and epsilon;
sigma=0 (as well as epsilon=0) would give an identically zero potential . See
sections 5.3.3 and 5.7.1 in the manual (version 4.0).<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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