Molecular Dynamics

Parse GROMACS .xvg files in Python and plot RMSD, RMSF and energy with a reusable read_xvg function. Start making publication-ready figures today.

Turn a GROMACS trajectory into a 2D free energy landscape with gmx sham and PCA. Start mapping your protein’s conformational basins in kJ/mol today.

Check what hardware molecular docking and MD really need: laptop specs, why GROMACS wants a CUDA GPU, and the free Colab and HPC routes students can use.

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 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.

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 clean a raw PDB for MD: rebuild missing loops, add hydrogens, and fix His, Asp and Cys protonation so your simulation does not crash.