Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations
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DOI：
10.1002/jcc.20387
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发表时间：
2006-04-30
影响因子：
3
通讯作者：
Feig, M
中科院分区：
文献类型：
--
作者：
Chocholousova, J;Feig, M
用GBMV（Generalized Born using Molecular Volume）和GBSW（Generalized Born with simple SWicking）方法对蛋白质和核酸系统的NVT和NVE模拟中不同的积分时间步长进行了测试。模拟的稳定性和能量守恒的影响与泊松理论的协议。结果发现，广义玻恩方法和泊松理论的基础上，常用的尖锐的分子表面定义的结果在分子动力学模拟协议与标准的2-fs时间步长的能量漂移和模拟文物之间的非常密切的协议。GBMV方法，它保持非常好的协议与泊松理论，同时提供能量守恒和稳定的模拟在1至1.5 fs的时间步长，提出了新的参数。(c)2006 Wiley Periodicals，Inc.
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. (c) 2006 Wiley Periodicals, Inc.