Moradi Mahmoud, Tajkhorshid Emad
Center for Biophysics and Computational Biology, Department of Biochemistry, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
J Phys Chem Lett. 2013 Jun 6;4(11):1882-1887. doi: 10.1021/jz400816x. Epub 2013 May 17.
We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measurements to gradually flatten the free-energy surface. The asymptotic convergence of the method is discussed, and several relations are derived for free-energy reconstruction and error estimation. Isomerization reaction of an atomistic polyproline peptide model is used to numerically illustrate the superior efficiency and faster convergence of the method compared with its adaptive-bias and driven components in isolation.
我们提出了一种新颖的自由能计算方法,该方法建设性地整合了两类不同的非平衡采样技术,即驱动(例如,引导分子动力学)和自适应偏置(例如,元动力学)方法。通过采用非平衡功关系,我们设计了一种具有明确依赖时间和历史的偏置的偏置协议,该协议使用实时功测量来逐渐使自由能表面变平。讨论了该方法的渐近收敛性,并推导了自由能重建和误差估计的几个关系。使用原子多聚脯氨酸肽模型的异构化反应进行数值说明,与单独的自适应偏置和驱动组件相比,该方法具有更高的效率和更快的收敛速度。