Molecular Dynamics: From Basics to Application [Article v1.0]

This tutorial equips natural scientists with the essential knowledge needed to utilize and comprehend molecular dynamics simulations effectively. Beginning with the stability of integration algorithms and the conservation of energy, this article proceeds with the description of atomistic forcefields, thermodynamic ensembles, long-range electrostatics treatment, and free energy calculations within molecular dynamics simulations. It then extends to the simulation of proteins and drug discovery applications. This comprehensive overview includes numerous references to relevant publications and tackles real-world problems. The tutorial is based on a 10-week master’s course typically undertaken by students in the first or second semester of their master’s program.