GROMACS

Build a protein-in-bilayer system with CHARMM-GUI Membrane Builder, then run the six-step equilibration ladder in GROMACS without rebuilding anything.

Set your GROMACS simulation box with gmx editconf. Choose cubic or dodecahedron, pick the right -d distance, and cut roughly 29 percent of your run time.

Learn to run gmx cluster with the gromos method and pull one defensible representative structure from your GROMACS trajectory.

Learn the exact gmx trjconv commands to remove PBC artifacts, center your protein, strip water, and extract single frames before you run any analysis.

Learn to run gmx pdb2gmx step by step, pick a force field and water model, and fix the “residue not found” error before your first MD run.

Run energy minimization in GROMACS with the exact em.mdp settings, grompp and mdrun commands, and convergence checks. Learn to read Fmax and fix EM errors.

Solvate a protein and add neutralizing ions in GROMACS with the exact gmx solvate, grompp and gmx genion commands. Fix the SOL group prompt that trips up beginners.

Run NVT then NPT equilibration in GROMACS with the exact commands, .mdp settings, and convergence checks. Learn why both phases matter and how to fix crashes.

Restart a crashed GROMACS run from its checkpoint and extend a short one with gmx convert-tpr. Learn the exact commands and fix the common errors.

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