We review the history of the parallel tempering simulation method. From its origins in data
analysis, the parallel tempering method has become a standard workhorse of …

The scope of this article is to present an overview of the Density Functional based Tight
Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and …

We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and
free energy methods in Amber18. Of particular interest is the development of alchemical free …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

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 …

Macromolecular and biomolecular folding landscapes typically contain high free energy
barriers that impede efficient sampling of configurational space by standard molecular …

Predicting protein structure solely from its amino acid sequence has long been a grand
challenge in structural biology and theoretical chemistry. 1–3 Exponentially increasing the …

An innovative replica exchange (parallel tempering) method called replica exchange with
solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented …

In complex systems with many degrees of freedom such as peptides and proteins, there
exists a huge number of local‐minimum‐energy states. Conventional simulations in the …

This book teaches modern Markov chain Monte Carlo (MC) simulation techniques step by
step. The material should be accessible to advanced undergraduate students and is suitable …