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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Berk,<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for your answer, I am happy to have the priority list for
how the van der Waals term of the pair potential is calculated.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>About fudgeQQ, do you mean that the pair potentials&#8217; coulomb
terms are scaled with the fudgeQQ value, even when &#8220;gen-pairs&#8221; is
set to &#8220;no&#8221;?<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>( I see from the manual that &#8220;FudgeLJ is only used when
generate pairs is set to &#8216;yes&#8217;, so maybe your answer is already
given in the manual. Actually, I am not sure if this statement is an implicit
information about FudgeQQ..)<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>-Soren<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</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"'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>Berk Hess<br>
<b>Sent:</b> Thursday, July 30, 2009 4:33 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> RE: [gmx-users] generate pair list and 1-4 interactions<o:p></o:p></span></p>

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<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Verdana","sans-serif"'>Hi,<br>
<br>
The charges are always scaled with fudgeQQ.<br>
<br>
For the LJ parameters the precendence is:<br>
<br>
For an atom pair in the [ pairs ] section with type A and B:<br>
if parameters are present on the line in the [ pairs ] section use those,
otherwise<br>
if parameters are present in the [ pairtypes ] section use those, otherwise<br>
if gen-pairs=no generate a fatal error, otherwise<br>
if parameters for A-B are present in the [ nonbond_params ] section scale with
fudgeLJ and use those, otherwise<br>
use the parameters for A and B in the [ atoms ] section and scale with fudgeLJ
and use those.<br>
<br>
Berk<o:p></o:p></span></p>

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<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Verdana","sans-serif"'>Date: Thu, 30 Jul 2009 15:58:40 +0800<br>
From: chees@nus.edu.sg<br>
To: gmx-users@gromacs.org<br>
Subject: [gmx-users] generate pair list and 1-4 interactions <o:p></o:p></span></p>

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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Dear
all,<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>I
am a bit confused about how the pair potentials (PPs)are calculated.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>&nbsp;<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>If
I state explicitly sigma and epsilon values for the pair potentials, can I then
still have a coulomb scaling of my 1-4 interactions?<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Say
I set &#8220;gen-pairs&#8221; to &#8220;yes&#8221;, although I have all
possible pair potential interactions specified under &#8220;[ pairtypes
]&#8221;, would I then still be able to scale my 1-4 coulomb interactions by
setting a &#8220;FudgeQQ&#8221; different from 1? Also, would I be able to
scale the already given van der Waals interactions with &#8220;FudgeLJ&#8221;?<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>&nbsp;<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Finally,
are generated pair potentials based on the parameters specified under &#8220;[
atomtypes ]&#8221; or &#8220;[ nonbond_params ]&#8221; (if the latter exist) in
the ffamber03nb.itp file?<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>&nbsp;<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Best
regards,<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Soren
Enemark<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>&nbsp;<o:p></o:p></span></p>

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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p>&nbsp;</o:p></span></p>

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