Molecular Modeling

Compare molecular docking and molecular dynamics: what a pose proves, what a trajectory adds, and why a defensible thesis project runs both in order.

Pick a defensible protein target and ligand set before you open AutoDock Vina. Follow the step-by-step selection checklist that survives a viva.

Pick a defensible MD simulation length and prove equilibration from RMSD, energy, temperature and pressure plateaus. Read the decision guide.

Turn your GROMACS run into a methods section a reviewer cannot reject. The exact parameters to report, real citations, and a worked example to adapt.

Turn a docked pose into a figure your supervisor accepts. Real PyMOL commands for cartoon-plus-sticks, labelled H-bonds, and a 300 dpi ray-traced render.

Stop copy-pasting em.mdp and md.mdp. Learn which GROMACS .mdp parameters you must choose deliberately, which to leave at defaults, and what breaks when you get them wrong.

Decode the GROMACS errors beginners actually hit: LINCS warnings, PBC artifacts, rtp mismatches and cut-off failures. Read the fix for each message.

Estimate protein-ligand binding free energy from a finished GROMACS trajectory with the free gmx_MMPBSA tool. Follow the step-by-step MM-PBSA workflow now.

Learn to run blind docking in AutoDock Vina to find an unknown binding site, from sizing a whole-protein box to clustering poses. Start the step-by-step guide.

Learn to choose between an experimental PDB structure, a SWISS-MODEL homology model, or AlphaFold for docking and MD, judged on coverage, confidence and fit.