18.8k citations · 35.1k across the 68 of their papers we have counts for
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Adding alchemical variables to metadynamics to enhance sampling in free energy calculations
Wei-Tse Hsu, Valerio Piomponi, Pascal T. Merz +2
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculation…
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
Cameron Abrams, Giovanni Bussi
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and…
Metadynamics with adaptive Gaussians
Davide Branduardi, Giovanni Bussi, Michele Parrinello
Metadynamics is an established sampling method aimed at reconstructing the free-energy surface relative to a set of appropriately chosen collective variables. In standard metadynam…
Nuclear quantum effects in solids using a colored-noise thermostat
Michele Ceriotti, Giovanni Bussi, Michele Parrinello
We present a method, based on a non-Markovian Langevin equation, to include quantum corrections to the classical dynamics of ions in a quasi-harmonic system. By properly fitting th…
Isothermal-isobaric molecular dynamics using stochastic velocity rescaling
Giovanni Bussi, Tatyana Zykova-Timan, Michele Parrinello
The authors present a new molecular dynamics algorithm for sampling the isothermal-isobaric ensemble. In this approach the velocities of all particles and volume degrees of freedom…
Langevin equation with colored noise for constant-temperature molecular dynamics simulations
Michele Ceriotti, Giovanni Bussi, Michele Parrinello
We discuss the use of a Langevin equation with a colored (correlated) noise to perform constant-temperature molecular dynamics simulations. Since the equations of motion are linear…
Optimal Langevin modelling of out-of-equilibrium molecular dynamics simulations
Cristian Micheletti, Giovanni Bussi, Alessandro Laio
We introduce a scheme for deriving an optimally-parametrised Langevin dynamics of few collective variables from data generated in molecular dynamics simulations. The drift and the…
Equilibrium free energies from non-equilibrium metadynamics
Giovanni Bussi, Alessandro Laio, Michele Parrinello
In this paper we propose a new formalism to map history-dependent metadynamics in a Markovian process. We apply this formalism to a model Langevin dynamics and determine the equili…
Canonical sampling through velocity-rescaling
Giovanni Bussi, Davide Donadio, Michele Parrinello
We present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random…
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
Alessandro Barducci, Giovanni Bussi, Michele Parrinello
We present a method for determining the free energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description whi…