Practical considerations for Molecular Dynamics

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.

Schedule

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.