Classical molecular dynamics is a computer simulation technique that is in widespread use
across many areas of science, from physics and chemistry to materials, biology, and …

Molecular dynamics simulation is now a widespread approach for understanding complex
systems on the atomistic scale. It finds applications from physics and chemistry to …

In this issue, Neale et al.(1) present a calculation of the free energy to bind an antimicrobial
peptide to a lipid bilayer using molecular dynamics simulations. This in itself is not unusual …

Since the 1960s, scientists have increasingly turned to molecular dynamics (MD) as a tool of
choice for studying complex and realistic condensed-matter systems. The reason behind this …

The quantitative assessment of uncertainty and sampling quality is essential in molecular
simulation. Many systems of interest are highly complex, often at the edge of current …

Growing computing capacity and algorithmic advances have facilitated the study of
increasingly large biomolecular systems at longer timescales. However, with these larger …

We propose a measure that quantifies the effort needed to compute a given stochastic
average, considered in the context of molecular modeling. This “difficulty index” is defined in …

It is increasingly widely recognized that ensemble-based approaches are required to
achieve reliability, accuracy, and precision in molecular dynamics calculations. The purpose …

The precision of several methods for computing the chemical potential by molecular
simulation is investigated. The study does not apply molecular simulation to the analysis but …

Markov state models are widely used to describe and analyze protein dynamics based on
molecular dynamics simulations, specifically to extract functionally relevant characteristic …