The Four-Days International Online Workshop on Molecular Dynamics Studies using AMBER Software provided a comprehensive introduction to biomolecular simulation techniques for researchers, faculty, and students in the fields of pharmaceutical sciences, chemistry, biophysics, and computational biology. The workshop covered essential concepts of molecular dynamics (MD) theory, system preparation, simulation execution, and trajectory analysis using the AMBER suite. Through hands-on demonstrations, participants learned how to build protein–ligand systems, apply minimization and equilibration protocols, run production MD, and perform key analyses such as RMSD, RMSF, radius of gyration, hydrogen-bond evaluation, and principal component analysis. The training also emphasized best practices for parameterization, quality control, and interpretation of MD results. By the end of the workshop, attendees gained practical skills enabling them to set up, run, and analyze molecular simulations for research and academic applications.
