Lipid bilayer simulations have long since been a holy grail in computational drug discovery. Given that membrane proteins are more than 60% of drug targets and 40% of drugs fail clinical trials due to poor membrane permeability, it is important to have a reliable model to properly model membrane simulations. One of the major challenges in Molecular Dynamics is the ability to accurately simulate an ion concentration gradient across a membrane in order to model diffusion which occurs on a large time scale. To address these issues, the need of a new periodic boundary condition, termed asymmetric periodic boundary conditions (ASP) is required to enhance computational sampling of our system. With these new conditions in place, an algorithm to help guide diffusion would be needed. To address the issue of diffusion, the development of positional center of mass constraints is needed to help assist molecules as they venture across the lipid bilayer.

Development of algorithms advancing all-atom lipid bilayer simulations

251st National Meeting (2016)

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