Trajectory Analysis
How to Do Principal Component Analysis (PCA) on a GROMACS Trajectory: Essential Dynamics for Beginners
Run PCA on a GROMACS trajectory with gmx covar and gmx anaeig to extract the dominant collective motions. Start building thesis-grade figures today.
How to Analyze Radius of Gyration, SASA and Hydrogen Bonds from a GROMACS Trajectory (Step-by-Step)
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.
How to Visualize a GROMACS Trajectory in VMD: A Step-by-Step Beginner’s Guide
Open your first GROMACS trajectory in VMD, fix the jumping-protein artifact, style a cartoon view, and export a movie. Watch your simulation move.