Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
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[1] J. Kirkwood. Statistical Mechanics of Fluid Mixtures , 1935 .
[2] J. Marcinkiewicz. Sur une propriété de la loi de Gauß , 1939 .
[3] P. Moran,et al. Mathematics of Statistics , 1948, Nature.
[4] H. Callen. Thermodynamics and an Introduction to Thermostatistics , 1988 .
[5] G. Torrie,et al. Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid , 1974 .
[6] S. Nosé. A unified formulation of the constant temperature molecular dynamics methods , 1984 .
[7] R. Callen,et al. Thermodynamics and an Introduction to Thermostatistics, 2nd Edition , 1985 .
[8] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[9] Alan M. Ferrenberg,et al. Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.
[10] Jan Hermans,et al. Simple analysis of noise and hysteresis in (slow-growth) free energy simulations , 1991 .
[11] Robert H. Wood,et al. Systematic errors in free energy perturbation calculations due to a finite sample of configuration space: sample-size hysteresis , 1991 .
[12] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[13] Berend Smit,et al. Understanding molecular simulation: from algorithms to applications , 1996 .
[14] K. Schulten,et al. Molecular dynamics study of unbinding of the avidin-biotin complex. , 1997, Biophysical journal.
[15] C. Jarzynski. Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach , 1997, cond-mat/9707325.
[16] C. Jarzynski. Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.
[17] K Schulten,et al. Reconstructing potential energy functions from simulated force-induced unbinding processes. , 1997, Biophysical journal.
[18] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[19] Laxmikant V. Kale,et al. NAMD2: Greater Scalability for Parallel Molecular Dynamics , 1999 .
[20] K Schulten,et al. Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[21] K. Schulten,et al. Reconstructing Potentials of Mean Force through Time Series Analysis of Steered Molecular Dynamics Simulations , 1999 .
[22] Benedict Leimkuhler,et al. Computational Molecular Dynamics: Challenges, Methods, Ideas , 1999, Computational Molecular Dynamics.
[23] K. Schulten,et al. Steered molecular dynamics and mechanical functions of proteins. , 2001, Current opinion in structural biology.
[24] G. Hummer,et al. Free energy reconstruction from nonequilibrium single-molecule pulling experiments , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[25] G. Hummer. Fast-growth thermodynamic integration: Error and efficiency analysis , 2001 .
[26] C. Jarzynski,et al. A “fast growth” method of computing free energy differences , 2001 .
[27] O. Becker,et al. Solvent effects on the energy landscapes and folding kinetics of polyalanine , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[28] Alexander D. MacKerell,et al. Computational Biochemistry and Biophysics , 2001 .
[29] K. Schulten,et al. Steered molecular dynamics investigations of protein function. , 2001, Journal of molecular graphics & modelling.
[30] K. Schulten,et al. Steered molecular dynamics studies of titin I1 domain unfolding. , 2002, Biophysical journal.
[31] Thomas B Woolf,et al. Theory of a systematic computational error in free energy differences. , 2002, Physical review letters.
[32] I. Tinoco,et al. Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality , 2002, Science.
[33] K. Schulten,et al. Energetics of glycerol conduction through aquaglyceroporin GlpF , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[34] Klaus Schulten,et al. Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics. , 2002, Journal of molecular biology.
[35] Daniel M. Zuckerman,et al. Overcoming finite-sampling errors in fast-switching free-energy estimates: extrapolative analysis of a molecular system , 2002 .
[36] Rommie E. Amaro,et al. Developing an energy landscape for the novel function of a (β/α)8 barrel: Ammonia conduction through HisF , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[37] K. Schulten,et al. Forced detachment of the CD2-CD58 complex. , 2003, Biophysical journal.
[38] 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 .