Molecular Dynamics Simulation with GROMACS

This two-half-day online course provides an overview of the fundamental workflow of molecular dynamics simulations using GROMACS on multi-node GPU clusters. It introduces the essential steps of energy minimization, equilibration, and production simulation, explains how force fields and parameterization define interactions. Finally the participants will learn how to analyze and visualize simulation results with VMD.
At the end of the course, participants will understand how to prepare a molecular system for simulation, how to run it efficiently on high-performance computing resources with GPUs across multiple nodes, and how to carry out basic trajectory analysis and visualization to extract meaningful structural and dynamical insights.