Partial differential equations and stochastic methods in molecular dynamics
T Lelievre, G Stoltz - Acta Numerica, 2016 - cambridge.org
The objective of molecular dynamics computations is to infer macroscopic properties of
matter from atomistic models via averages with respect to probability measures dictated by …
matter from atomistic models via averages with respect to probability measures dictated by …
Tinker 8: software tools for molecular design
The Tinker software, currently released as version 8, is a modular molecular mechanics and
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …
Molecular dynamics
For a number of years, we have been exploring the underpinnings of algorithms for
simulating molecular dynamics from a mathematics perspective, ie as outsiders. We have …
simulating molecular dynamics from a mathematics perspective, ie as outsiders. We have …
[BOOK][B] Free energy computations: A mathematical perspective
This monograph provides a general introduction to advanced computational methods for
free energy calculations, from the systematic and rigorous point of view of applied …
free energy calculations, from the systematic and rigorous point of view of applied …
Robust and efficient configurational molecular sampling via Langevin dynamics
A wide variety of numerical methods are evaluated and compared for solving the stochastic
differential equations encountered in molecular dynamics. The methods are based on the …
differential equations encountered in molecular dynamics. The methods are based on the …
Unified efficient thermostat scheme for the canonical ensemble with holonomic or isokinetic constraints via molecular dynamics
We have recently proposed a new unified theoretical scheme (the “middle” scheme) for
thermostat algorithms for efficient and accurate configurational sampling of the canonical …
thermostat algorithms for efficient and accurate configurational sampling of the canonical …
Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation
Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties
of matter. In complex condensed-phase systems, however, it is difficult to design Monte …
of matter. In complex condensed-phase systems, however, it is difficult to design Monte …
Sampling in constrained domains with orthogonal-space variational gradient descent
Sampling methods, as important inference and learning techniques, are typically designed
for unconstrained domains. However, constraints are ubiquitous in machine learning …
for unconstrained domains. However, constraints are ubiquitous in machine learning …
Monte Carlo on manifolds: sampling densities and integrating functions
We describe and analyze some Monte Carlo methods for manifolds in euclidean space
defined by equality and inequality constraints. First, we give an MCMC sampler for …
defined by equality and inequality constraints. First, we give an MCMC sampler for …
A computational method to extract macroscopic variables and their dynamics in multiscale systems
This paper introduces coordinate-independent methods for analyzing multiscale dynamical
systems using numerical techniques based on the transfer operator and its adjoint. In …
systems using numerical techniques based on the transfer operator and its adjoint. In …