Calculation of Collective Variable-based PMF by Combining WHAM with Umbrella Sampling

作     者：XU Wei-Xin LI Yang ZHANG John Z.H. 徐维新;李阳;张增辉

作者机构：State Key Laboratory of Precision SpectroscopyDepartment of PhysicsEast China Normal UniversityShanghai 200062 Institute of Theoretical and Computational ScienceInstitutes for Advanced Interdisciplinary ResearchEast China Normal UniversityShanghai 200062 Department of ChemistryNew York UniversityNew YorkNew York 10003USA 

出 版 物：《Chinese Physics Letters》 (中国物理快报（英文版）)

年 卷 期：2012年第29卷第6期

页      面：291-294页

核心收录：

学科分类：07[理学] 070202[理学-粒子物理与原子核物理] 0702[理学-物理学] 

基　　金：Supported by the National Natural Science Foundation of China under Grant Nos 21003048,10974054,and 20933002 Shanghai Pujiang Program(09PJ1404000) 

主　　题：coordinates utilized calculating 

摘      要：Potential of mean force (PMF) with respect to localized reaction coordinates (RCs) such as distance is often applied to evaluate the free energy profile along the reaction pathway for complex molecular ***,calculation of PMF as a function of global RCs is still a challenging and important problem in computational *** examine the combined use of the weighted histogram analysis method and the umbrella sampling method for the calculation of PMF as a function of a global RC from the coarse-grained Langevin dynamics simulations for a model *** method yields the folding free energy profile projected onto a global RC,which is in accord with benchmark *** this method rare global events would be sufficiently sampled because the biased potential can be used for restricting the global conformation to specific regions during free energy *** strategy presented can also be utilized in calculating the global intra- and intermolecular PMF at more detailed levels.