2.4. Analysis

Note

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

• 2.4.1. Pairwise RMSD
• 2.4.2. Antechamber
• 2.4.3. Export Dry Trajectory (no water)
• 2.4.4. parmchk2.sh
• 2.4.5. parmed
• 2.4.6. Principal Component Analysis
• 2.4.7. Plot PMF with PyMBAR
• 2.4.8. RDF
• 2.4.9. Root Mean Square Deviation (RMSD)