Molecular Dynamics

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.

Eight scoped, finishable GROMACS molecular dynamics project ideas for an MSc thesis, each with a research question, deliverable, and difficulty. Pick yours and start.

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.

Compare GROMACS, AMBER, NAMD, OpenMM and LAMMPS on license, GPU, and beginner-friendliness. See the best free MD engine for students and start learning.