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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'>Few years ago, C. Neale (thanks to him!) posted in
the GROMACS mailing list a very useful tutorial [1] to scale the Coulombic 1-4
interactions when we combine forcefields with different fudgeLJ and fudgeQQ
values. I am trying to apply this trick to a system containing a peptide and a
micelle simulated with AMBER99SB-ILDN and GLYCAM force fields, respectively
(see my previous message [2]). <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 have followed all the steps described in [2] and
computed the sigma_ij and epsilon_ij values for the peptide and the micelle
with comb_rules 2 (i.e. sigma_ij=1/2(sigma_i+sigma_j) and
epsilon_ij=sqrt(epsilon_i*epsilon_j). The epsilon_i and sigma_i are taken from
the [ atomtypes ] section in the ffnonbonded.itp file<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'>However, in the step 3 in [2], it is said that the
peptide the pair interaction values (i.e. epsilon) should be divided by 10 and
these "values/12" include in the pairtypes section. I suspect a typo
here. Indeed, if I set the general fudgeLJ and fudgeQQ to 1.0 and 0.1666666, I
should have a ratio of 10 (for (0.83333/(0.166666)))*1/2 for epsilon_ij and not
"12". Am I right?<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'>To test the changes, I have performed three nsteps=0
runs in NVT ensemble for a simple system (1 peptide and 1 glycolipid solvated
in water) with the initial and modified and non-modified nonbonded parameters:<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- With ffnonbbonded.itp file non-modified with
fudgeLJ=0.5 and fudgeQQ=0.83333 --- > peptide<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- With ffnonbbonded.itp file non-modified with
fudgeLJ=1.0 and fudgeQQ=1.0 --- > micelle<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- With ffnonbbonded.itp file modified with
fudgeLJ=1.0 and fudgeQQ=0.1666666 --- > 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'>and compared the *.trr files obtained from these the three
runs. <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'>The only differences I found are, indeed, in the
force section of the *.trr files for atoms involved in the modified pair
section. To be sure that my modifications are corrects, I would like to obtain
the individual pair energy values of the micelle and the peptide. How to obtain
this values? <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]
http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html<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]
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html<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 again for your help and advices. <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>
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