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Canonical sampling through velocity rescaling.
The authors 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 factor.Expand
PLUMED 2: New feathers for an old bird
TLDR
We present PLUMED 2, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables. Expand
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
TLDR
We present a program aimed at free-energy calculations in molecular systems. Expand
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 which has metadynamicsExpand
Accurate sampling using Langevin dynamics.
We show how to derive a simple integrator for the Langevin equation and illustrate how it is possible to check the accuracy of the obtained distribution on the fly, using the concept of effectiveExpand
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
We review a selection of methods for performing enhanced sampling in 1 molecular dynamics simulations. We consider methods based on collective variable biasing 2
Isothermal-isobaric molecular dynamics using stochastic velocity rescaling.
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 are rescaled by aExpand
Hamiltonian replica exchange in GROMACS: a flexible implementation
A simple and general implementation of Hamiltonian replica exchange for the popular molecular dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can beExpand
Colored-Noise Thermostats à la Carte
Recently, we have shown how a colored-noise Langevin equation can be used in the context of molecular dynamics as a tool to obtain dynamical trajectories whose properties are tailored to displayExpand
Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.
We develop a new free-energy method, based on the combination of parallel tempering and metadynamics, and apply this method to the calculation of the free-energy landscape of the folding beta hairpinExpand
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