• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

Equilibrium free energies from fast-switching trajectories with large time steps.

作者信息

Lechner Wolfgang, Oberhofer Harald, Dellago Christoph, Geissler Phillip L

机构信息

Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.

出版信息

J Chem Phys. 2006 Jan 28;124(4):044113. doi: 10.1063/1.2162874.

DOI:10.1063/1.2162874
PMID:16460155
Abstract

Jarzynski's [Phys. Rev. Lett. 78, 2690 (1997)] identity for the free-energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase-space mappings. Solving a system's equation of motion by approximate means generates a mapping that is perfectly valid for this purpose, regardless of how closely the solution mimics true time evolution. We exploit this fact, using crudely dynamical trajectories to compute free-energy differences that are in principle exact. Numerical simulations show that Newton's equation can be discretized to low order over very large time steps (limited only by the computer's ability to represent resulting values of dynamical variables) without sacrificing thermodynamic accuracy. For computing the reversible work required to move a particle through a dense liquid, these calculations are more efficient than conventional fast-switching simulations by more than an order of magnitude. We also explore consequences of the phase-space mapping perspective for systems at equilibrium, deriving an exact expression for the statistics of energy fluctuations in simulated conservative systems.

摘要

相似文献

1
Equilibrium free energies from fast-switching trajectories with large time steps.
J Chem Phys. 2006 Jan 28;124(4):044113. doi: 10.1063/1.2162874.
2
Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?非平衡轨迹的偏差采样:快速切换模拟能否优于传统自由能计算方法?
J Phys Chem B. 2005 Apr 14;109(14):6902-15. doi: 10.1021/jp044556a.
3
Estimation of free-energy differences from computed work distributions: an application of Jarzynski's equality.从计算得到的功分布估计自由能差:雅可比等式的应用。
J Phys Chem B. 2012 Sep 13;116(36):10986-95. doi: 10.1021/jp300527q. Epub 2012 Aug 30.
4
Ordering of limits in the Jarzynski equality.
J Chem Phys. 2006 Feb 7;124(5):054117. doi: 10.1063/1.2165187.
5
Optimizing the switching function for nonequilibrium free-energy calculations: an on-the-fly approach.优化非平衡自由能计算的切换函数:一种实时方法。
J Chem Phys. 2009 May 7;130(17):174705. doi: 10.1063/1.3126602.
6
Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics.通过炼金术绝热分子动力学实现高效精确的溶剂化自由能
J Chem Phys. 2006 Aug 21;125(7):074115. doi: 10.1063/1.2232082.
7
Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations.非哈密顿分子动力学模拟中广义克鲁克斯非平衡功定理的数值验证。
J Chem Phys. 2007 Jul 21;127(3):034110. doi: 10.1063/1.2749257.
8
Assessing the efficiency of free energy calculation methods.评估自由能计算方法的效率。
J Chem Phys. 2004 Feb 22;120(8):3563-78. doi: 10.1063/1.1642607.
9
Optimizing the driving function for nonequilibrium free-energy calculations in the linear regime: a variational approach.线性区域非平衡自由能计算中驱动函数的优化:一种变分方法。
J Chem Phys. 2005 Mar 8;122(10):104106. doi: 10.1063/1.1860556.
10
Computation of the nonhomogeneous equilibrium states of a rigid-rod solution.刚性棒状溶液非均匀平衡态的计算。
J Chem Phys. 2006 Dec 7;125(21):214906. doi: 10.1063/1.2403130.

引用本文的文献

1
Entropy, Free Energy, and Work of Restricted Boltzmann Machines.受限玻尔兹曼机的熵、自由能与功
Entropy (Basel). 2020 May 11;22(5):538. doi: 10.3390/e22050538.
2
Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.多时间步双哈密顿混合分子动力学-蒙特卡罗正则传播算法。
J Chem Theory Comput. 2016 Apr 12;12(4):1449-1458. doi: 10.1021/acs.jctc.5b00706. Epub 2016 Mar 25.
3
Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.非平衡路径蒙特卡罗是一种用于平衡模拟的有效工具。
Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):E1009-18. doi: 10.1073/pnas.1106094108. Epub 2011 Oct 24.
4
Replica exchange with nonequilibrium switches.非平衡开关复制交换法
Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12224-9. doi: 10.1073/pnas.0900406106. Epub 2009 Jul 10.
5
Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.计算熵和自由能的方法及其在涉及蛋白质柔性和配体结合问题中的应用。
Curr Protein Pept Sci. 2009 Jun;10(3):229-43. doi: 10.2174/138920309788452209.
6
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.存在仪器噪声时基于非平衡功数据的自由能贝叶斯估计。
J Chem Phys. 2008 Jul 14;129(2):024102. doi: 10.1063/1.2937892.