If you landed on CompChems from a search result, this page tells you where to go next based on what you’re trying to do. Each path below points to a series: an ordered list of articles you can read top to bottom.
If you want to learn the theory
The pedagogical walk through molecular dynamics: force fields, integrators, ensembles, thermostats, periodic boundary conditions. Beginner → advanced.
If you want to run your first GROMACS simulation
The end-to-end tutorial path: installation, file formats, the .mdp file, and a complete protein-in-water walkthrough with downloadable inputs.
If you have a trajectory and need to analyze it
RMSD, RMSF, hydrogen bonds, SASA, clustering, energy properties, each with the gmx command and a Python plotting example.
If you want to visualize results
PyMOL for publication-quality figures, VMD for trajectory inspection.
→ PyMOL Beginner Series → VMD Analysis Series
If you want coarse-grained MD
Working with the Martini force field in GROMACS: soluble and membrane systems.
Stuck or have a topic to suggest? Reach me at info@compchems.com.