Efficient “Middle” Thermostat Scheme …
281
61. Valsson O, Parrinello M (2014) Variational approach to enhanced sampling and free energy
calculations. Phys Rev Lett 113(9):090601
62. Valsson O, Tiwary P, Parrinello M (2016) Enhancing important fluctuations: Rare events and
metadynamics from a conceptual viewpoint. Annu Rev Phys Chem 67(1):159–184
63. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding.
Chem Phys Lett 314(1):141–151
64. Peters B (2017) Reaction rate theory and rare events simulations. Elsevier, Amsterdam,
Netherlands
65. Carter EA, Ciccotti G, Hynes JT, Kapral R (1989) Constrained reaction coordinate dynamics
for the simulation of rare events. Chem Phys Lett 156(5):472–477
66. Sprik M, Ciccotti G (1998) Free energy from constrained molecular dynamics. J Chem Phys
109(18):7737–7744
67. Sergi A, Ciccotti G, Falconi M, Desideri A, Ferrario M (2002) Effective binding force calculation in a dimeric protein by molecular dynamics simulation. J Chem Phys 116(14):6329–6338
68. Bello-Rivas JM, Elber R (2015) Exact milestoning. J Chem Phys 142(9):094102
69. Anandakrishnan R, Drozdetski A, Walker Ross C, Onufriev Alexey V (2015) Speed of conformational change: Comparing explicit and implicit solvent molecular dynamics simulations.
Biophys J 108(5):1153–1164
281
61. Valsson O, Parrinello M (2014) Variational approach to enhanced sampling and free energy
calculations. Phys Rev Lett 113(9):090601
62. Valsson O, Tiwary P, Parrinello M (2016) Enhancing important fluctuations: Rare events and
metadynamics from a conceptual viewpoint. Annu Rev Phys Chem 67(1):159–184
63. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding.
Chem Phys Lett 314(1):141–151
64. Peters B (2017) Reaction rate theory and rare events simulations. Elsevier, Amsterdam,
Netherlands
65. Carter EA, Ciccotti G, Hynes JT, Kapral R (1989) Constrained reaction coordinate dynamics
for the simulation of rare events. Chem Phys Lett 156(5):472–477
66. Sprik M, Ciccotti G (1998) Free energy from constrained molecular dynamics. J Chem Phys
109(18):7737–7744
67. Sergi A, Ciccotti G, Falconi M, Desideri A, Ferrario M (2002) Effective binding force calculation in a dimeric protein by molecular dynamics simulation. J Chem Phys 116(14):6329–6338
68. Bello-Rivas JM, Elber R (2015) Exact milestoning. J Chem Phys 142(9):094102
69. Anandakrishnan R, Drozdetski A, Walker Ross C, Onufriev Alexey V (2015) Speed of conformational change: Comparing explicit and implicit solvent molecular dynamics simulations.
Biophys J 108(5):1153–1164