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.
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.
| 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 Preparing 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.