Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …

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 term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

Modern problems in astronomical Bayesian inference require efficient methods for sampling
from complex, high-dimensional, often multimodal probability distributions. Most popular …

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 …

We describe the Multiscale Modeling Tools for Structural Biology (MMTSB) Tool Set (), which
is a novel set of utilities and programming libraries that provide new enhanced sampling and …

We present the latest version of the Groningen Molecular Simulation program package,
GROMOS05. It has been developed for the dynamical modelling of (bio) molecules using …

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 …

An algorithm is proposed that generates a set of temperatures for use in parallel tempering
simulations (also known as temperature-replica exchange molecular dynamics simulations) …

We develope 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 …