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Pick a scoped, defensible molecular docking project you can finish with free tools and public data. Start building your thesis today.

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.

Calculate backbone RMSD and per-residue RMSF from a GROMACS trajectory with gmx rms and gmx rmsf, then read the plots. Start analyzing your MD results.

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.