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Calculate backbone RMSD and per-residue RMSF from a GROMACS trajectory with gmx rms and gmx rmsf, then read the plots. Start analyzing your MD results.

Open your first GROMACS trajectory in VMD, fix the jumping-protein artifact, style a cartoon view, and export a movie. Watch your simulation move.

Turn a docked pose into a real protein-ligand trajectory in GROMACS. Build the ligand topology, solvate, equilibrate, and run. Start your MD project.

Eight scoped, finishable GROMACS molecular dynamics project ideas for an MSc thesis, each with a research question, deliverable, and difficulty. Pick yours and start.

Run your first protein MD simulation in GROMACS end to end, from PDB file to production trajectory. Follow the exact lysozyme-in-water commands today.

Install GROMACS the right way on Linux, Windows (WSL2), or free Google Colab. Follow the exact commands and run your first gmx check today.

Run molecular docking in your browser, set up AutoDock Vina in a free Google Colab notebook, dock from any laptop, and pull your results back. Start today.

Learn how to read molecular docking results, what the kcal/mol binding affinity means, why more negative is stronger, and how to prove a pose is trustworthy.

Learn molecular docking in PyRx step by step, load your protein, prep ligands with Open Babel, run AutoDock Vina, and read binding affinities. No command line.

Learn AutoDock Vina step by step, prepare files, set the grid box, run docking, and read binding affinity scores. Start your first job today.