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quickstart
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HPC
python
simulation
More Notes !!
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1. Theory / Methods Overview
6. Tutorial
6.1. Simple MD Tutorial of Alanine Dipeptide
6.2. Applying Distance Restraints in Classical MD Simulations
6.3. QM/MM Simulation of the Claisen Rearrangment Reaction
7. Analysis
7.1. Pairwise RMSD
7.2. Antechamber
7.3. Export Dry Trajectory (no water)
7.4. parmchk2.sh
7.5. parmed
7.6. Principal Component Analysis
7.7. Plot PMF with PyMBAR
7.8. RDF
7.9. Root Mean Square Deviation (RMSD)
7.10. Root Mean Square Fluctuation (RMSF)
7.11. tleap
simulation
7.
Analysis
7.
Analysis
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For up-to-date examples, please see
van-richard/amberassist
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