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Enhanced sampling methods for molecular dynamics simulations
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …
molecular dynamics simulations and allow the sampling of larger portions of the …
Metadynamics
Metadynamics is a powerful technique for enhancing sampling in molecular dynamics
simulations and reconstructing the free‐energy surface as a function of few selected …
simulations and reconstructing the free‐energy surface as a function of few selected …
Hyperactive learning for data-driven interatomic potentials
Data-driven interatomic potentials have emerged as a powerful tool for approximating ab
initio potential energy surfaces. The most time-consuming step in creating these interatomic …
initio potential energy surfaces. The most time-consuming step in creating these interatomic …
Rethinking metadynamics: from bias potentials to probability distributions
Metadynamics is an enhanced sampling method of great popularity, based on the on-the-fly
construction of a bias potential that is a function of a selected number of collective variables …
construction of a bias potential that is a function of a selected number of collective variables …
The adaptive biasing force method: Everything you always wanted to know but were afraid to ask
In the host of numerical schemes devised to calculate free energy differences by way of
geometric transformations, the adaptive biasing force algorithm has emerged as a promising …
geometric transformations, the adaptive biasing force algorithm has emerged as a promising …
Free energy methods for the description of molecular processes
C Chipot - Annual Review of Biophysics, 2023 - annualreviews.org
Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …
relevant to biophysics have been considerably enhanced by the contribution of statistical …
Well-tempered metadynamics: a smoothly converging and tunable free-energy method
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 …
collective variables using an adaptive bias. The formalism provides a unified description …
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
Here we present a program aimed at free-energy calculations in molecular systems. It
consists of a series of routines that can be interfaced with the most popular classical …
consists of a series of routines that can be interfaced with the most popular classical …
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
Metadynamics is a powerful algorithm that can be used both for reconstructing the free
energy and for accelerating rare events in systems described by complex Hamiltonians, at …
energy and for accelerating rare events in systems described by complex Hamiltonians, at …
Exploration vs convergence speed in adaptive-bias enhanced sampling
In adaptive-bias enhanced sampling methods, a bias potential is added to the system to
drive transitions between metastable states. The bias potential is a function of a few …
drive transitions between metastable states. The bias potential is a function of a few …