Advanced Molecular Dynamics Simulations of Protein Structure using GROMACS

Molecular dynamics (MD) simulations are at the forefront of computational biology and biophysics, enabling researchers to explore the structural and functional dynamics of biomolecules. This 3-day workshop on Advanced Molecular Dynamics Simulations of Protein Structure using GROMACS is crafted for students, researchers, and professionals aiming to delve deep into protein dynamics and molecular interactions using GROMACS—one of the most widely used open-source MD engines.

The workshop progresses from the fundamentals of molecular dynamics and software setup to real-case-based simulation workflows and advanced analysis techniques. Learners will gain hands-on experience with PDB preparation, system solvation, energy minimization, equilibrations, and post-processing, including RMSD, RMSF, hydrogen bonding, and trajectory visualization. By the end of the program, participants will be equipped to carry out high-quality molecular dynamics simulations independently and contribute effectively to research or industry projects.