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quickstart
scripting
simulations
More Notes !!
Google Scholar
GitHub
Twitter
Linkedin
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2.1. Theory / Methods Overview
2.1.4.1. Binding Affinity
2.1.4.2. Classical Molecular Dynamics
2.1.4.3. FE Alchem
2.1.4.5. Free Energy Estimators
2.1.4.6. QM/MM Simulations
2.2. Compile Notes
2.2.1. Compile
helpmelib
executable
2.2.2. Compiling Amber
2.2.3. Install QMHub
2.2.4. TorchMDnet-ext Environment (CPU)
2.3. Tutorial
2.3.1. Simple MD Tutorial of Alanine Dipeptide
2.3.2. Applying Distance Restraints in Classical MD Simulations
2.3.3. QM/MM Simulation of the Claisen Rearrangment Reaction
2.4. Analysis
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)
2.
simulations
2.4.
Analysis
2.4.6.
Principal Component Analysis
#
example with PyTraj
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