Marsili Simone, Barducci Alessandro, Chelli Riccardo, Procacci Piero, Schettino Vincenzo
Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy.
J Phys Chem B. 2006 Jul 27;110(29):14011-3. doi: 10.1021/jp062755j.
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.
我们提出了一种用于复杂系统分子动力学模拟中伞形采样方法的新途径。通过生成单个自适应轨迹来实现对慢自由度的加速采样，该轨迹利用从系统先前历史导出的时间相关偏置势，倾向于均匀地跨越反应坐标。为了展示该方法的收敛行为和效率，我们给出了水中丙氨酸二肽的自由能表面作为主链二面角的函数。
