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