Molecular Dynamics

Run gmx dssp on your GROMACS trajectory, read the .dat and .xvg outputs, and fix the “do_dssp not found” error that breaks every old tutorial.

Predict how a point mutation changes protein stability with DynaMut2, mCSM and DDMut, and learn to read the ddG sign correctly before you report it.

Mutate a residue in PyMOL, save the mutant correctly, then run a fair wild-type vs mutant MD comparison in GROMACS without overclaiming the result.

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.