Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange.
暂无分享,去创建一个
[1] Lula Rosso,et al. Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics. , 2006, The Journal of chemical physics.
[2] Charles H. Bennett,et al. Efficient estimation of free energy differences from Monte Carlo data , 1976 .
[3] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[4] J. Haile,et al. Determination of Excess Gibbs Free Energy from Computer Simulation: Multiple-Parameter Charging Approach , 1987 .
[5] R. Zwanzig. High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .
[6] Jed W. Pitera,et al. A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations , 2002 .
[7] C. Predescu,et al. On the efficiency of exchange in parallel tempering monte carlo simulations. , 2004, The journal of physical chemistry. B.
[8] F. Young. Biochemistry , 1955, The Indian Medical Gazette.
[9] S. Takada,et al. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction , 2002 .
[10] A. Mark,et al. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations , 1994 .
[11] R. Levy,et al. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. , 1998, Annual review of physical chemistry.
[12] Michael R. Shirts,et al. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins , 2003 .
[13] R. Swendsen,et al. Comparison of free energy methods for molecular systems. , 2006, The Journal of chemical physics.
[14] David A. Kofke,et al. Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling , 2001 .
[15] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[16] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[17] Tomoyasu Tanaka. Methods of Statistical Physics , 2002 .
[18] Daniel M. Zuckerman,et al. Systematic Finite-Sampling Inaccuracy in Free Energy Differences and Other Nonlinear Quantities , 2002 .
[19] J. Hopfield,et al. Entropy‐enthalpy compensation: Perturbation and relaxation in thermodynamic systems , 1996 .
[20] Berend Smit,et al. Understanding molecular simulation: from algorithms to applications , 1996 .
[21] Charles L. Brooks,et al. λ‐dynamics: A new approach to free energy calculations , 1996 .
[22] J. Ilja Siepmann,et al. Novel Configurational-Bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-Atom Description of Branched Alkanes , 1999 .
[23] R. Wolfenden,et al. Interaction of the peptide bond with solvent water: a vapor phase analysis. , 1978, Biochemistry.
[24] Berend Smit,et al. Understanding Molecular Simulation , 2001 .
[25] C. Jarzynski. Rare events and the convergence of exponentially averaged work values. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.
[26] Michael R. Shirts,et al. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. , 2005, The Journal of chemical physics.
[27] Justin L. MacCallum,et al. Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field , 2003, J. Comput. Chem..
[28] David L Mobley,et al. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. , 2007, The journal of physical chemistry. B.
[29] 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.
[30] William L. Jorgensen,et al. Accuracy of free energies of hydration using CM1 and CM3 atomic charges , 2004, J. Comput. Chem..
[31] J. Kirkwood. Statistical Mechanics of Fluid Mixtures , 1935 .
[32] Michael R. Shirts,et al. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. , 2005, The Journal of chemical physics.
[33] Abraham M Lenhoff,et al. Solvation free energy of amino acids and side-chain analogues. , 2007, The journal of physical chemistry. B.
[34] Wei Yang,et al. Generalized ensembles serve to improve the convergence of free energy simulations , 2003 .
[35] M. Kenward,et al. An Introduction to the Bootstrap , 2007 .
[36] Gerard T. Barkema,et al. Monte Carlo Methods in Statistical Physics , 1999 .
[37] D. Chandler,et al. Introduction To Modern Statistical Mechanics , 1987 .