de Groot B L, van Aalten D M, Amadei A, Berendsen H J
Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biophysical Chemistry, University of Groningen, The Netherlands.
Biophys J. 1996 Oct;71(4):1707-13. doi: 10.1016/S0006-3495(96)79372-4.
A detailed investigation is presented into the effect of limited sampling time and small changes in the force field on molecular dynamics simulations of a protein. Thirteen independent simulations of the B1 IgG-binding domain of streptococcal protein G were performed, with small changes in the simulation parameters in each simulation. Parameters studied included temperature, bond constraints, cut-off radius for electrostatic interactions, and initial placement of hydrogen atoms. The essential dynamics technique was used to reveal dynamic differences between the simulations. Similar essential dynamics properties were found for all simulations, indicating that the large concerted motions found in the simulations are not particularly sensitive to small changes in the force field. A thorough investigation into the stability of the essential dynamics properties as derived from a molecular dynamics simulation of a few hundred picoseconds is provided. Although the definition of the essential modes of motion has not fully converged in these short simulations, the subspace in which these modes are confined is found to be reproducible.
本文详细研究了有限采样时间和力场微小变化对蛋白质分子动力学模拟的影响。对链球菌蛋白G的B1 IgG结合结构域进行了13次独立模拟，每次模拟的参数都有微小变化。研究的参数包括温度、键约束、静电相互作用的截止半径以及氢原子的初始位置。使用主成分动力学技术揭示模拟之间的动态差异。所有模拟都发现了相似的主成分动力学特性，这表明模拟中发现的大规模协同运动对力场的微小变化不太敏感。本文还对从几百皮秒的分子动力学模拟中得出的主成分动力学特性的稳定性进行了深入研究。尽管在这些短模拟中运动主模式的定义尚未完全收敛，但发现这些模式所限制的子空间是可重复的。
