Reviews and Other Readings

Atomistic Molecular Dynamics Simulations

• Best Practices for Foundations in Molecular Simulations [Article v1.0]
• Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]
• From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0](also available as an online tutorial)
• Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]

Enhanced Sampling Methods

• Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]
• Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint
• Enhanced sampling without borders: on global biasing functions and how to reweight them
• Using metadynamics to explore complex free-energy landscapes
• Metadynamics: A Unified Framework for Accelerating Rare Events and Sampling Thermodynamics and Kinetics
• Analyzing and Biasing Simulations with PLUMED (also arXiv:1812.08213)

Collective Variables

• Reaction coordinates in complex systems-a perspective
• Collective Variables for Crystallization Simulations-from Early Developments to Recent Advances
• Critical comparison of general-purpose collective variables for crystal nucleation

Machine Learning for Finding Collective Variables

• Manifold Learning in Atomistic Simulations: A Conceptual Review
• Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems
• Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation
• Chasing collective variables using temporal data-driven strategies
• Machine learning approaches for analyzing and enhancing molecular dynamics simulations