Strategic Issues in Molecular Dynamics Simulations of Membranes
The heterogeneity associated with membrane systems poses a huge challenge for computer simulations of membrane dynamics and structure. Unlike proteins or nucleic acids with well-defined three-dimensional structures, membrane components such as lipid bilayers derive a vast majority of their properties and function from their fluid nature. This introduces the problem of setting up the correct bilayer model system for any realistic computer simulation. The model includes: choice of the system size; interatomic force fields; treatment of short and long-range interactions; and, most important, the macroscopic boundary conditions that best mimic experimental conditions. The simulation is thus an integral part of the model.
KeywordsMolecular Dynamics Simulation Lipid Bilayer Membrane Strategic Issue Dipole Potential Fast Multipole Method
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