This is the workshop material for a Molecular Dynamics course that is being developed and delivered by the Digital Research Alliance of Canada’s Molecular Modelling and Simulation Team.
This is the workshop material for a Molecular Dynamics course that is being developed and delivered by the Digital Research Alliance of Canada’s Molecular Modelling and Simulation Team.
| Setup | Download files required for the lesson | |
| 00:00 | 1. Force Fields and Interactions |
What is Molecular Dynamics and how can I benefit from using it?
What is a force field? What mathematical energy terms are used in biomolecular force fields? |
| 00:30 | 2. Fast Methods to Evaluate Forces |
Why the computation of non-bonded interactions is the speed limiting factor?
How are non-bonded interactions computed efficiently? What is a cutoff distance? How to choose the appropriate cutoff distance? |
| 01:00 | 3. Advancing Simulation in Time |
How is simulation time advanced in a molecular dynamics simulation?
What factors are limiting a simulation time step? How to accelerate a simulation? |
| 01:20 | 4. Periodic Boundary Conditions | How to simulate a bulk (gas, liquid or solid) system by using only a small part? |
| 01:40 | 5. Degrees of Freedom |
How is kinetic energy contained and distributed in a dynamic molecular system
Why constraints are used in MD simulations, and how they can affect dynamics |
| 01:50 | 6. Electrostatic Interactions | How electrostatic interactions are calculated in periodic systems? |
| 02:00 | 7. Controlling Temperature |
What is temperature on the molecular level?
Why do we want to control the temperature of our MD-simulations? What temperature control algorithms are commonly used? What are the strengths and weaknesses of these common thermostats? |
| 02:20 | 8. Controlling Pressure |
Why do we want to control the pressure of our MD-simulations?
What pressure control algorithms are commonly used? What are the strengths and weaknesses of these common barostats? |
| 02:30 | 9. Water models |
Why do we want to use water in out simulations?
What water models are commonly used? How to chose a model of water for a simulation? |
| 02:45 | 10. End of Workshop | Break |
| 03:45 | 11. Supplemental: Overview of the Common Force Fields |
What are the categories of molecular dynamics force fields?
What force fields are available? What systems they work best with? |
| 03:45 | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.