Self-healing umbrella sampling: A non-equilibrium approach for quantitative free energy calculations
Self-healing umbrella sampling: A non-equilibrium approach for quantitative free energy calculations
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DOI：
10.1021/jp062755j
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发表时间：
2006-07-27
影响因子：
3.3
通讯作者：
Schettino, Vincenzo
中科院分区：
文献类型：
--
作者：
Marsili, Simone;Barducci, Alessandro;Schettino, Vincenzo
提出了一种用于复杂系统分子动力学模拟的伞式采样方法。慢自由度的加速采样是通过产生一个单一的自适应轨迹来实现的，该轨迹倾向于均匀地跨越反应坐标，使用来自系统先前历史的时间相关偏置势。为了证明该方法的收敛性和效率，我们给出了丙氨酸二肽在水中的自由能面作为主二面角的函数。
We propose a new approach for the umbrella sampling method in molecular dynamics simulations of complex systems. An accelerated sampling of the slow degrees of freedom is achieved by generating a single self-adaptive trajectory that tends to span uniformly the reaction coordinate using a time dependent bias potential derived from the preceding history of the system. To show the convergent behavior and the efficiency of the method, we present the free energy surface of alanine dipeptide in water as a function of the backbone dihedral angles.