Walker Ross C, Crowley Michael F, Case David A
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
J Comput Chem. 2008 May;29(7):1019-31. doi: 10.1002/jcc.20857.
Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many nanoseconds. The link atom approach used for treating the QM/MM boundary shows improved performance, and the user interface has been rewritten to bring the format into line with classical MD simulations. Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge density functional tight binding (SCC-DFTB) method. Performance has been improved to the point where using QM/MM, for a QM system of 71 atoms within an explicitly solvated protein using periodic boundaries and PME requires less than twice the cpu time of the corresponding classical simulation.
Amber模拟程序的第9版包含一种新的半经验混合量子力学/分子力学（QM/MM）功能。这包括对隐式溶剂（广义玻恩）的支持，以及对使用新开发的粒子网格埃瓦尔德（PME）方法的QM/MM实现进行周期性显式溶剂模拟的支持。该代码提供了足够精确的梯度，以便运行许多纳秒的恒定能量QM/MM分子动力学（MD）模拟。用于处理QM/MM边界的连接原子方法表现出更好的性能，并且用户界面已被重写，以使格式与经典MD模拟一致。支持PM3、PDDG/PM3、PM3CARB1、AM1、MNDO和PDDG/MNDO半经验哈密顿量以及自洽电荷密度泛函紧束缚（SCC-DFTB）方法。性能已经提升到这样的程度：对于一个使用周期性边界和PME在显式溶剂化蛋白质中的71个原子的QM系统，使用QM/MM所需的CPU时间不到相应经典模拟的两倍。
