Molecular dynamics simulation primer for: Introduction to atomistic modeling and simulation of biomolecular systems

Molecular dynamics (MD) and related techniques have been used for computer simulations of biomolecular systems for over 40 years, but only recently due to advances in computer hardware, simulation software and methodologies, as well as breakthroughs in structural biology, have they become a widely-used tool for studying the molecular mechanisms of biological function and its modulation. This dataset represents a primer for learning basic MD simulation setup and analysis using a prototypical K+ channel KcsA embedded in a hydrated lipid bilayer. The dataset includes files necessary for setup of MD simulations using CHARMM-GUI web toolkit, running them using nanoscale MD (NAMD) and analysing using visual MD (VMD) sofware. Detailed explanations are provided in the book chapter "Introduction to Atomistic Modeling and Simulation of Biomolecular Systems" to be published soon.