Luginbühl P, Güntert P, Billeter M, Wüthrich K
Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
J Biomol NMR. 1996 Sep;8(2):136-46. doi: 10.1007/BF00211160.
A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.
介绍了一种用于生物大分子分子动力学（MD）模拟和能量优化的新程序OPAL。结合用于MD轨迹分析的支持程序TRAJEC，OPAL在处理不同力场时具有高效性和灵活性，并提供用户友好的界面和广泛的轨迹分析功能。显著特点包括在诸如NEC SX-3等向量超级计算机上高达1.5 GFlops的计算速度、用于在显式溶剂中进行研究以减小系统大小的椭球边界以及对静水压力的自然处理。通过对纯水的MD模拟、在不同溶剂模型中对突变型大肠杆菌谷氧还蛋白与谷胱甘肽的混合二硫键的NMR结构进行能量最小化以及使用瞬时或时间平均NMR约束或无约束对小蛋白信息素Er-2进行MD模拟，展示了OPAL的实际应用。
