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<p class=MsoPlainText><span lang=EN-US>This is to report some results that I
have been recently obtaining with the G53a6 parameterization of DPPC and also to
ask for advice. I have read in the mailing list that perhaps this parameterization
is worse than that of Tieleman/Berger to reproduce bilayer properties but I
didn’t think that differences would be so serious:<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-US>I have been doing bilayers simulations at
different temperatures between 298 and 353 K with semiisotropic pressure
control at 1 bar using a Parrinello-Rahman or a Berendsen barostat, with SPC or
SPCE waters, with PME or cutoff, using also different initial structures
including that of the Tieleman web page as well as my own bilayers, and several
combinations of all these variables. Actually I did all this to tune simulations
conditions to study the adsorption of other molecules to the bilayer… The
important thing is that regardless the employed initial conditions and
simulation parameters the DPPC bilayer using the G53a6 parameterization quickly
reduces the available area per lipid, increases its width and the palmitoyl
chains become completely straight and tight definitely loosing the fluid phase
at any of the employed temperatures. I repeated some of the abovementioned
tests using the Tieleman parameterization and it does not present this problem.
Moreover, I used a modified itp for DMPC, based on that of DPPC for 53a6 (just
cutting the atoms that exceed and closing the chains with CH3 groups) and it
seems to work much better than G53a6-DPPC although the area per lipid is
perhaps a bit small… These results have independently been reproduced by
a colleague from another institution that used her own mdp/pdb/top files.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>My conclusion is that this parametrization
should not be used, at least for DPPC bilayers… and I would question also
the use of DMPC with G53a6... although I am not sure with this lipid. I want to
ask for advice from experts in bilayers to confirm all this. Assuming that all
is true, what would be the best parameters set to simulate membrane proteins or
peptides in bilayers? More specifically, is it correct to use the G53a6
parameterization of the GROMOS ff combined with the Tieleman parameters for the
lipids?<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Thanks for any comment,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Angel Piņeiro.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
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