Molecular Dynamics Simulation of Phospholipid Bilayers

  • Scott Feller
Chapter
Part of the Biological Physics Series book series (BIOMEDICAL)

Abstract

During the past decade advances in computational hardware and simulation methodologies have moved the field of molecular dynamics (MD) simulation at an incredible pace. There is no better example of this development than the MD simulation of lipid membranes. An early ‘membrane’ simulation examined the behavior of water molecules, between surfaces composed of lipids molecules frozen in place, for a total of 8 picoseconds (ps) [1]. A pioneering work representing the membrane interior in atomic detail is the simulation of van der Ploeg and Berendsen where a decanoate bilayer (without solvent) was followed for 80 ps [2]. Today, bilayer simulations describing both lipid and solvent in full atomic detail are commonplace, with recent reports of trajectories of length 10 nanoseconds (ns) [3,4]. While MD simulation in general has grown with advances in processing power, the lipid simulation field has especially benefited because membrane simulations typically include a large number of molecules in the system. Additionally, several algorithmic developments have increased the quality of lipid simulations. These include methods such as particle mesh Ewald (PME) summation [5] for the accurate calculation of Coulombic intermolecular forces between lipid headgroups and water, constant pressure ensembles that allow dynamic adjustment of membrane size and shape [6], and multiple time step algorithms that promise order of magnitude increases in simulation length [7].

Keywords

Hydrate Hydrocarbon Carbonyl Alkane Boiling 

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© Springer-Verlag Berlin Heidelberg 2001

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  • Scott Feller

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