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w-REXAMD: A HamiltonianReplica Exchange Approachto Improve Free Energy Calculations for Systems with Kinetically TrappedConformations

机译：w-REXAMD：哈密顿量副本交换方法改进有动圈闭系统的自由能计算构型

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Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy calculations, relative to conventional MD, using windowed accelerated MD within a Hamiltonian replica exchange framework (w-REXAMD). We show that for a case in which multiple conformations are separated by large free energy barriers, w-REXAMD is a useful enhanced sampling technique, without any necessary reweighting.

机译：自由能支配着许多生物过程的平衡程度。分离自由能极小值的高壁垒通常会限制分子动力学（MD）模拟中的采样，从而导致不正确的自由能。在这里，我们展示了在汉密尔顿式副本交换框架（w-REXAMD）中使用加窗加速的MD相对于常规MD的增强采样和改进的自由能计算。我们表明，对于多个构象被较大的自由能垒隔开的情况，w-REXAMD是一种有用的增强采样技术，无需进行任何必要的加权。

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期刊名称 ACS AuthorChoice
作者
Mehrnoosh Arrar; *; Cesar Augusto F. de Oliveira; Mikolai Fajer; ∥; William Sinko; J. Andrew McCammon;
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年(卷),期 -1(9),1
年度 -1
页码 18–23
总页数 6
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1. w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations [J] . Mehrnoosh Arrar, Cesar Augusto F. de Oliveira, Mikolai Fajer Journal of chemical theory and computation: JCTC . 2013,第1期

机译：w-REXAMD：哈密顿副本交换方法，以改善具有运动学陷阱构象的系统的自由能计算
2. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation [J] . Huang Yu-ming M., McCammon J. Andrew, Miao Yinglong Journal of chemical theory and computation: JCTC . 2018,第4期

机译：副本交换高斯加速的分子动力学：提高增强的采样和自由能计算
3. Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling [J] . Peter Carlsson, Lennart Nilsson Journal of Computational Chemistry: Organic, Inorganic, Physical, Biological . 2003,第12期

机译：使用lambda缩放的原子质量并分离构象和变换采样的小型系统，提高了自由能计算的精度和效率
4. Potential and Orbital Functionals: Analytic Energy Gradients for OEP and Self-Interaction-Free Exchange-Correlation Energy Functional for Thermochemistry and Kinetics [C] . Weitao Yang Advances in Computational Methods in Sciences and Engineering 2005 vol.4B; Lecture Series on Computer and Computational Sciences; vol.4B . 2005

机译：势能和轨道功能：OEP的解析能梯度和热化学和动力学的无自相互作用交换相关能量能
5. A calculation of the doubly differential cross section for inclusive pion - helium-4 double charge exchange at incident pion kinetic energy less than 270 MeV. [D] . Kulkarni, Arun Venkatesh. 1994

机译：在入射小子动能小于270 MeV时，包含性小子-氦4双电荷交换的双微分截面的计算。
6. Replica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculation [O] . Yu-ming M. Huang, J. Andrew McCammon, Yinglong Miao -1

机译：副本交换高斯加速的分子动力学：改进的增强采样和自由能计算
7. An Improved Potential Energy Surface for the H2Cl System and Its Use for Calculations of Rate Coefficients and Kinetic Isotope Effects [O] . Allison, Thomas C., Lynch, Gillian C., Truhlar, Donald G., 1996

机译：改进的H2Cl体系势能面及其在计算速率系数和动力学同位素效应中的用途
8. On the Correlation of the Kinetics of Electron Transfer Processes with the Change in Reaction Free Energy. Application to Electron-Exchange Initiated Chemiluminescence Reactions. [R] . Schuster, G. B. 1979

机译：电子转移过程动力学与反应自由能变化的相关性。电子交换引发化学发光反应的应用。

w-REXAMD: A HamiltonianReplica Exchange Approachto Improve Free Energy Calculations for Systems with Kinetically TrappedConformations

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