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.
Chocholousová
Jana
J
Department of Biochemistry and Molecular Biology, Michigan State University, 218 Biochemistry Building, East Lansing, Michigan 48824-1319, USA.
Feig
Michael
M
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D055672:Static Electricity; D013499:Surface Properties
D010455:Peptides; D011506:Proteins; D004247:DNA