Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations

Different integrator time steps in {NVT} and {NVE} simulations of protein and nucleic acid systems are tested with the {GBMV} {(Generalized} Born using Molecular Volume) and {GBSW} {(Generalized} Born with simple {SWitching)} methods. The simulation stability and energy conservation is investigated in relation to the agreement with the Poisson theory. It is found that very close agreement between generalized Born methods and the Poisson theory based on the commonly used sharp molecular surface definition results in energy drift and simulation artifacts in molecular dynamics simulation protocols with standard 2-fs time steps. New parameters are proposed for the {GBMV} method, which maintains very good agreement with the Poisson theory while providing energy conservation and stable simulations at time steps of 1 to 1.5 fs. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 719-729, 2006