Towards all-atoms sampling of membrane configurations using non-equilibrium molecular dynamics.

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In all-atoms simulations, phenomena that can be observed are limited in terms of time-scale, usually up to a few µs. This means that slow processes taking place on a longer time-scale are not observable. Here, we develop a method to generate all-atoms configurations of membrane. The diffusion of the lipids within the membrane is not simulated per say, but non-equilibrium molecular dynamics is used to exchange the positions of the lipids in the membrane. With Monte-Carlo exchanges performed with alchemical transformation, different possible configurations of the membrane at the thermodynamic equilibrium are generated. It becomes possible to perform an equilibration of the membrane in all-atoms representations at a reduced sampling cost, and thus get a more precise model of the membrane organization. This algorithm could also be employed to decipher specific lipid binding sites modulating the function on membrane proteins