Molecular Modeling

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.

Learn to superimpose two proteins in PyMOL with align, super and cealign, read the RMSD, pick the right command, and fix zero-atom 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.

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.

Learn to convert PDB to PDBQT, MOL2, SDF and SMILES with Open Babel and get your docking files ready 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.