Hyperdynamics made simple: Accelerated molecular dynamics with the Bond-Boost method

Subsurface Nitrogen Dissociation Kinetics in Lithium Metal from Metadynamics

“…Metadynamics is one such method, used for accelerating and reconstructing free energy surfaces from molecular simulations, including first-principles simulations involving chemical reactions. − ,, More recently, metadynamics has been used for directly calculating rate constants. − This approach, sometimes called “infrequent metadynamics”, accelerates the time scale of simulations by adding an artificial bias while keeping the critical transition state regions unbiased. − Under the assumptions of transition state theory, it has been shown that the addition of the artificial bias accelerates the time scale of the simulation by a factor α as defined in eq where k B is Boltzmann’s constant, T is temperature, t sim is the simulation time, which is the sum of the time steps taken in the simulation, t phys is the corresponding accelerated physical or real time, s ( t sim ) is the value of one (or more) collective variable(s) s at simulation time t sim , V ( s ( t sim ), t sim ) is the instantaneous value of the added artificial bias potential V at collective variable value s ( t sim ) and simulation time t sim , and the brackets ⟨···⟩ denote the average of the bracketed quantity over the course of the simulation. , The physical elapsed time t phys is therefore a statistical property of the simulation, depending exponentially on the added artificial bias potential. ,,, The exponential dependence of the acceleration factor on the artificial bias allows for substantial acceleration of the time scale, but also leads to potentially noisy or biased reaction rate estimates if the bias potential grows too rapidly or if the collective variables chosen are not sufficient. ,, In particular, the resulting rate estimates can be erroneous or difficult to interpret when the collective variables chosen are insufficient for describing important barriers or configurations that may exist within the initial state. , It should be noted that this “hidden barriers” problem is not unique to the context of calculating rate constants; this is also a well-known cause of error in the ordinary usage of metadynamics for reconstructing free energy surfaces. ,…”

Generating conformational transition paths with low potential-energy barriers for proteins

“…However, the time taken for these simulations risks to be too long before a system reaches one of the transition states which are rare, short-lived and associated with high-energy barriers [6]. Hence, recent developments focus on accelerating these simulation techniques by manipulating temperature, energy or forces [7][8][9][10][11][12].…”

Improved scaling of temperature-accelerated dynamics using localization

“…However, due to the small time step for time evolution, MD is typically limited to times of the order of microseconds, while many crucial atomistic processes occur on much longer time scales. As a result, a variety of accelerated dynamics methods have been developed, including hyperdynamics, 4,5,[14][15][16][17]32 parallel replica dynamics, [6][7][8][9] temperature-accelerated dynamics (TAD), [10][11][12][13] metadynamics, [21][22][23][24] basin-searching, [26][27][28][29][30][31] and -dynamics. 25 In particular, TAD simulations of small systems have been shown to lead to speed-ups of 4-6 orders of magnitude compared to molecular dynamics.…”