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 didnt 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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