Colored-noise thermostats à la carte

Abstract

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 display desired sampling features. In the present paper, after having reviewed some analytical results for the stochastic differential equations forming the basis of our approach, we describe in detail the implementation of the generalized Langevin equation thermostat and the fitting procedure used to obtain optimal parameters. We discuss in detail the simulation of nuclear quantum effects, and demonstrate that, by carefully choosing parameters, one can successfully model strongly anharmonic solids such as neon. For the reader's convenience, a library of thermostat parameters and some demonstrative code can be downloaded from an on-line repository.

References in corpus (5)

• Canonical sampling through velocity-rescaling
• Accurate sampling using Langevin dynamics
• Nuclear quantum effects in solids using a colored-noise thermostat
• Stochastic thermostats: comparison of local and global schemes
• Quantum thermal transport from classical molecular dynamics

Cited by in corpus (22)

• Efficient stochastic thermostatting of path integral molecular dynamics
• How to remove the spurious resonances from ring polymer molecular dynamics
• Efficient first-principles calculation of the quantum kinetic energy and momentum distribution of nuclei
• Accelerating the convergence of path integral dynamics with a generalized Langevin equation
• Iterative Reconstruction of Memory Kernels
• Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances
• Uncertainty estimation for molecular dynamics and sampling
• Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol
• Recognizing Local and Global Structural Motifs at the Atomic Scale
• Zero-Point Energy Leakage in Quantum Thermal Bath Molecular Dynamics Simulations
• Nuclear quantum effects in ab initio dynamics: theory and experiments for lithium imide
• On the Applicability of the Caldeira-Leggett Model to Condensed Phase Vibrational Spectroscopy
• Converged Colored Noise Path Integral Molecular Dynamics Study of the Zundel Cation down to Ultra-low Temperatures at Coupled Cluster Accuracy
• Applications of the Generalised Langevin Equation: towards a realistic description of the baths
• Finite-temperature materials modeling from the quantum nuclei to the hot electrons regime
• Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
• Static disorder and structural correlations in the low temperature phase of lithium imide
• Quantifying the impact of vibrational nonequilibrium in plasma catalysis: Insights from a molecular dynamics model of dissociative chemisorption
• Assessing the persistence of chalcogen bonds in solution with neural network potentials
• Quantum Vibronic Effects on the Excitation Energies of the Nitrogen-Vacancy Center in Diamond
• Simulating nuclear and electronic quantum effects in enzymes
• Isotope effects in x-ray absorption spectra of liquid water