Trajectory Analysis

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.

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.

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.

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