Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
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DOI：
10.1063/1.2716389
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发表时间：
2007-04-14
影响因子：
4.4
通讯作者：
Shalloway, David
中科院分区：
文献类型：
--
作者：
West, Anthony M. A.;Elber, Ron;Shalloway, David
说明了最近引入的计算算法，用于扩展原子详细模拟的时间尺度。该算法称为里程碑，基于将动力学划分为“里程碑”之间的一系列轨迹，并为沿反应坐标的运动构建非马尔可夫模型。封闭丙氨酸的构象转变动力学经过计算，结果显示准确，比直接的分子动力学效率高约 9 倍，并且是非指数的。一般的缩放参数预测扩散过程的里程碑数量会线性加速，而越过障碍的过渡会呈指数加速。该算法的并行化也很简单。作为一个附带结果，里程碑还产生沿反应坐标的自由能分布，并且能够描述沿一个（或几个）自由度的非平衡运动。 (c) 2007 年美国物理研究所。
A recently introduced computational algorithm to extend time scales of atomically detailed simulations is illustrated. The algorithm, milestoning, is based on partitioning the dynamics to a sequence of trajectories between "milestones" and constructing a non-Markovian model for the motion along a reaction coordinate. The kinetics of a conformational transition in a blocked alanine is computed and shown to be accurate, more efficient than straightforward molecular dynamics by a factor of about 9, and nonexponential. A general scaling argument predicts a linear speedup with the number of milestones for diffusive processes and an exponential speedup for transitions over barriers. The algorithm is also trivial to parallelize. As a side result, milestoning also produces the free energy profile along the reaction coordinate and is able to describe nonequilibrium motions along one (or a few) degrees of freedom. (c) 2007 American Institute of Physics.