3. Analysis

Note

For up-to-date examples, please see van-richard/amberassist

• 3.1. Pairwise RMSD
• 3.2. Antechamber
• 3.3. Export Dry Trajectory (no water)
• 3.4. PCA with CPPTRAJ
• 3.5. parmchk2.sh
• 3.6. parmed
• 3.7. Principal Component Analysis
• 3.8. Plot PMF with PyMBAR
• 3.9. RDF
• 3.10. Root Mean Square Deviation (RMSD)
• 3.11. Root Mean Square Fluctuation (RMSF)
• 3.12. tleap