Premium
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations
Author(s) -
Chocholoušová Jana,
Feig Michael
Publication year - 2006
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20387
Subject(s) - molecular dynamics , integrator , poisson distribution , statistical physics , stability (learning theory) , rotation formalisms in three dimensions , representation (politics) , mathematics , energy (signal processing) , computer science , physics , computational chemistry , chemistry , quantum mechanics , geometry , statistics , voltage , machine learning , politics , political science , law
Different integrator time steps in NVT and NVE simulations of protein and nucleic acid systems are tested with the GBMV ( G eneralized B orn using M olecular V olume) and GBSW ( G eneralized B orn with simple SW itching) 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