Free Energy Computations: A Mathematical Perspective

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Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. (2016, background): “Here we only consider linear combinations of Cartesian coordinates; however, it is possible to derive ICF for arbitrary collective variables, though this leads to significantly more complex equations [110].”
Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation (2011, methodology): “where we have used a velocity Verlet discretization of the BBK integrator [40, 36].”
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics (2016, methodology): “● Hybrid Monte Carlo and variants, such as Generalized hybrid Monte Carlo (GHMC) [25], a Metropolized form of Langevin dynamics.”
Generalisation of the Eyring–Kramers Transition Rate Formula to Irreversible Diffusion Processes (2015, background): “On the one hand, it is known [41] that rescaling time by 1/γ and letting γ → +∞, (qt)t≥0 converges to the overdamped Langevin process dx t = −u′(x t)dt + √ 2 dwt, (5.”
Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022, methodology): “In the Colvars implementation, this is done by solving a Poisson equation [46, 66, 224].”