[gmx-users] G53a6 parameterization for DPPC

Ángel Piñeiro angel.pineiro at usc.es
Tue Sep 2 09:48:58 CEST 2008

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:


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.


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?


Thanks for any comment,


Angel Piñeiro.


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