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Code of Conduct
Setup
Episodes
An Overview of Information Flow in AMBER
Checking and Preparing PDB Files
Assigning Protonation States to Residues in a Protein
Solvating a System, Adding Ions and Generating Input Files
Running Molecular Dynamics Simulations with AMBER
Preparation and simulation of membrane and membrane-protein systems
End of Workshop
Hands-on 1: Packing a complex mixture of different lipid species into a bilayer and simulating it
Hands-on 2: Transferring AMBER simulation to GROMACS
Hands-on 3A: Preparing a Complex RNA-protein System
Hands-on 3B: Simulating a Complex RNA-protein System
Hands-on 4: Preparing a system for simulation with GROMACS
Hands-on 5: Generating topologies and parameters for small molecules.
Hands-on 6: A Comparative Performance Ranking of the Molecular Dynamics Software
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Running Molecular Dynamics on Alliance clusters with AMBER
: Instructor Notes
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