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<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Dear All, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>I try to apply the half double pair list method for a
system containing a glycolipid surfactant and a peptide modeled with the GLYCAM
and AMBER99SB force field. Briefly what I did : <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>1- I have changed the forcefield.itp like this <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>[ defaults ]<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>; gen_pairs set explicitly ---> gen-pairs =
"no"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>; nbfunc
comb-rule
gen-pairs fudgeLJ fudgeQQ<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>;1
2
yes 0.5
0.8333 -</span></font><font size=2 face=Wingdings><span lang=EN-US
style='font-size:10.0pt;font-family:Wingdings'>à</span></font><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>
for AMBER99SB only<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>1
2
no 1.0
0.16666666666666 --- > for both GLYCAM et AMBER99SB<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>;1
2
yes
1.0 1.0 </span></font><font size=2 face=Wingdings><span
lang=EN-US style='font-size:10.0pt;font-family:Wingdings'>à</span></font><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>
for GLYCAM only<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>#include "ffnonbonded_mod.itp"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>#include "ffbonded.itp"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>2- For the surfactant, I have calculated the
pair-types interactions manually with the comb-rule = 2 and divided the values
/6 and added these values in [pairtypes] section in the ffnonbonded_mod.itp
files<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>3- For the peptide, I have calculated the pair-types interactions
manually comb-rule = 2 and divided the values /10 and added these values in [pairtypes]
section in the ffnonbonded_mod.itp files. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>4- In the surfactant topology file I have repeated 6 times
the [pairs] directives 0.166666*6 ~=10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>5 - In the peptide topology file I have repeated 5
times the [pairs] directives 0.166666*5 ~= </span></font><font size=2
face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>0.8333<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Is it correct ?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>However I have a little doubt about “</span></font><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>gen-pairs”
directive should I have set it to “no” or “yes”. in a
previous message with a similar problem, the gen directive was set “yes”
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><a
href="http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html">http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html</a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Thank you for your help<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Stephane<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
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