Molecular Modeling

Write a docking methods section a reviewer accepts. Get the reporting checklist plus a worked, copy-adaptable AutoDock Vina example.

Set the AutoDock Vina grid box the right way: find the binding-site center, pick a box size in Angstroms, and stop guessing coordinates. Start docking today.

Run a full GROMACS molecular dynamics simulation on Google Colab’s free GPU, no local install. Set up the runtime, install GROMACS, and save your trajectory.

Run PCA on a GROMACS trajectory with gmx covar and gmx anaeig to extract the dominant collective motions. Start building thesis-grade figures today.

Measure compactness, solvent exposure and H-bonds from a GROMACS trajectory with gmx gyrate, gmx sasa and gmx hbond. Start analyzing your MD run today.

Learn how to build a GROMACS-ready ligand topology. Compare CGenFF, ACPYPE and ATB, then prepare a defensible protein-ligand system step by step.

Decide which force field to pick at the GROMACS pdb2gmx step. Compare CHARMM36, AMBER and OPLS, and learn to justify your choice in a thesis.

Open your first GROMACS trajectory in VMD, fix the jumping-protein artifact, style a cartoon view, and export a movie. Watch your simulation move.

Turn a docked pose into a real protein-ligand trajectory in GROMACS. Build the ligand topology, solvate, equilibrate, and run. Start your MD project.

Run your first protein MD simulation in GROMACS end to end, from PDB file to production trajectory. Follow the exact lysozyme-in-water commands today.