This lesson is being piloted (Beta version)

ab initio MD

This lesson by the Molecular Sciences Software Institute(MolSSI) teaches users fundamentals of scientific programming used in computational molecular sciences. The material is designed for undergraduate students, or other early career students, who have no prior programming experience. To see the full MolSSI’s education mission statement, please see here.

This lesson is under development, please report issues to the GitHub repository


Students should be familiar with opening the Terminal window and creating and navigating files in bash.


Setup Download files required for the lesson
00:00 1. Introduction How can we simulate the motion of molecules subject to realistic intramolecular forces?
00:30 2. _ab_ _initio_ potential energy surface How do we obtain realistic intramolecular forces?
01:30 3. Finding the equilibrium bond length How do we find the equilibrium bond length of our diatomic molecule?
01:45 4. Force Constant for Harmonic Potential How do we define the force constant of a diatomic molecule?
02:00 5. Computing the harmonic frequency How do we use information about the ab initio potential energy surface to estimate the vibrational frequency of a diatomic molecule??
02:30 6. Velocity Verlet Algorithm How do we practically solve Newton’s equations of motion?
04:00 7. Optional Lesson on Choosing intial bond-length and velocity How do we initialize the position and velocity of the atoms for our molecular dynamics simulation?
05:00 8. Running the molecular dynamics simulation! What does the molecular dynamics simulation tell us?
05:50 Finish

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