Escorted free energy simulations.
暂无分享,去创建一个
[1] Charles H. Bennett,et al. Efficient estimation of free energy differences from Monte Carlo data , 1976 .
[2] B. Efron,et al. The Jackknife: The Bootstrap and Other Resampling Plans. , 1983 .
[3] D. Sherrington. Stochastic Processes in Physics and Chemistry , 1983 .
[4] P. Strevens. Iii , 1985 .
[5] B. Efron. The jackknife, the bootstrap, and other resampling plans , 1987 .
[6] D. Chandler,et al. Introduction To Modern Statistical Mechanics , 1987 .
[7] Peter A. Kollman,et al. The lag between the Hamiltonian and the system configuration in free energy perturbation calculations , 1989 .
[8] Jan Hermans,et al. Simple analysis of noise and hysteresis in (slow-growth) free energy simulations , 1991 .
[9] Robert H. Wood,et al. Estimation of errors in free energy calculations due to the lag between the hamiltonian and the system configuration , 1991 .
[10] Thomas M. Cover,et al. Elements of Information Theory , 2005 .
[11] W. Reinhardt,et al. Variational path optimization and upper and lower bounds to free energy changes via finite time minimization of external work , 1992 .
[12] William P. Reinhardt,et al. A finite‐time variational method for determining optimal paths and obtaining bounds on free energy changes from computer simulations , 1993 .
[13] W. Ebeling. Stochastic Processes in Physics and Chemistry , 1995 .
[14] Leonard M. Sander,et al. Scaling and river networks: A Landau theory for erosion , 1997 .
[15] C. Jarzynski. Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.
[16] G. Crooks. Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems , 1998 .
[17] G. Crooks. Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[18] Mark A. Miller,et al. Efficient free energy calculations by variationally optimized metric scaling: Concepts and applications to the volume dependence of cluster free energies and to solid–solid phase transitions , 2000 .
[19] T. Fearn. The Jackknife , 2000 .
[20] G. Crooks. Path-ensemble averages in systems driven far from equilibrium , 1999, cond-mat/9908420.
[21] Berend Smit,et al. Understanding Molecular Simulation , 2001 .
[22] Thomas B Woolf,et al. Theory of a systematic computational error in free energy differences. , 2002, Physical review letters.
[23] Berend Smit,et al. Accelerating Monte Carlo Sampling , 2002 .
[24] C. Jarzynski. Targeted free energy perturbation. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.
[25] Michael R. Shirts,et al. Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. , 2003, Physical review letters.
[26] Benedict J. Leimkuhler,et al. Generating generalized distributions from dynamical simulation , 2003 .
[27] F. Ritort,et al. Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[28] D. Zuckerman,et al. Single-ensemble nonequilibrium path-sampling estimates of free energy differences. , 2004, The Journal of chemical physics.
[29] D. Kofke,et al. Rosenbluth-sampled nonequilibrium work method for calculation of free energies in molecular simulation. , 2005, The Journal of chemical physics.
[30] 宁北芳,et al. 疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .
[31] David A. Kofke,et al. On the sampling requirements for exponential-work free-energy calculations , 2006 .
[32] C. Jarzynski. Rare events and the convergence of exponentially averaged work values. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.
[33] Christophe Chipot,et al. Free Energy Calculations , 2008 .
[34] G. Crooks,et al. Length of time's arrow. , 2008, Physical review letters.
[35] C. Jarzynski,et al. Escorted free energy simulations: improving convergence by reducing dissipation. , 2008, Physical review letters.
[36] H. Then,et al. Using bijective maps to improve free-energy estimates. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.
[37] Suriyanarayanan Vaikuntanathan,et al. Dissipation and lag in irreversible processes , 2009, 0909.3457.
[38] David D. L. Minh. Density-dependent analysis of nonequilibrium paths improves free energy estimates. , 2009, The Journal of chemical physics.
[39] Christophe Chipot,et al. Good practices in free-energy calculations. , 2010, The journal of physical chemistry. B.
[40] H. Then,et al. Measuring the convergence of Monte Carlo free-energy calculations. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.
[41] W. Marsden. I and J , 2012 .
[42] Journal of Chemical Physics , 1932, Nature.