Molecular Modeling

Decide which force field to pick at the GROMACS pdb2gmx step. Compare CHARMM36, AMBER and OPLS, and learn to justify your choice in a thesis.

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.

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.

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.

Learn how to prepare a protein and ligand for docking, clean the PDB, add hydrogens and charges, and export PDBQT files. Get docking-ready today.

Compare the best free molecular docking software for students in 2026 (AutoDock Vina, SwissDock, DiffDock). See costs, GPU needs and where to start.