Running Molecular Dynamics on Alliance clusters with AMBER

This is the workshop material for a Molecular Dynamics course that is being developed and delivered by Compute Canada’s Molecular Modelling and Simulation Team.

Schedule

Setup Download files required for the lesson
00:00 1. An Overview of Information Flow in AMBER What files are needed to run an MD simulation with AMBER?
00:35 2. Checking and Cleaning PDB Files What problems are commonly found in PDB files?
Why fixing errors in PDB files is essential for a simulation?
01:05 3. Assigning Protonation States to Residues in a Protein Why titratable aminoacid residues can have different protonation states?
How to determine protonation state of a residue in a protein?
What are the weaknesses of fixed protonation state simulations?
01:45 4. Solvating a System, Adding Ions and Generating Input Files Why the simulation system should be neutralized?
How to add water and ions to a simulation system?
How to choose size and shape of a solvent box?
02:20 5. Running Molecular Dynamics Simulations with AMBER What simulation programs are available in the AMBER package?
How to minimize energy?
How to heat up a simulation system?
How to equilibrate a simulation system?
02:55 6. Preparation and simulation of membrane and membrane-protein systems How to prepare a membrane simulation system?
How to pack a protein in a lipid bilayer?
03:30 7. End of Workshop Break
04:30 8. Hands-on 1: Packing a complex mixture of different lipid species into a bilayer and simulating it How to pack a complex mixture of different lipid species into a bilayer?
How to minimize energy?
How to heat up a simulation system?
How to equilibrate a simulation system?
05:05 9. Hands-on 2: Transferring AMBER simulation to GROMACS How to use GROMACS to continue a simulation equilibrated with AMBER?
05:30 10. Hands-on 3A: Preparing a Complex RNA-protein System How to add missing segments to a protein?
How to add missing segments to a nucleic acid?
How to align molecules with VMD?
06:05 11. Hands-on 3B: Simulating a Complex RNA-protein System How to simulate with AMBER?
06:40 12. Hands-on 4: Preparing a system for simulation with GROMACS How to Prepare Input Files for Simulation with GROMACS?
07:15 13. Hands-on 5: Generating topologies and parameters for small molecules. How to parameterize small molecules?
07:50 14. Hands-on 6: A Comparative Performance Ranking of the Molecular Dynamics Software How to evaluate CPU efficiency of a simulation?
How fast and efficient my simulation will run with different programs and computing resources?
08:25 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.