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Coarse graining of membrane simulations by translating atomistic dynamics to densities
and fields with Milestoning is discussed. The space of the membrane system is divided
into cells and the different cells are characterized by order parameters presenting
the number densities. The dynamics of the order parameters are probed with Milestoning.
The methodology is illustrated here for a phospholipid membrane system (a hydrated
bilayer of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) lipid molecules). Significant
inhomogeneity in membrane internal number density leads to complex free energy landscape
and local maps of transition times. Dynamics and distributions of cavities within
the membrane assist the permeation of nonpolar solutes such as xenon atoms. It is
illustrated that quantitative and detailed dynamics of water transport through DOPC
membrane can be analyzed using Milestoning with fields. The reaction space for water
transport includes at least two slow variables: the normal to the membrane plane,
and the water density.