Molecular simulations are predominantly ran under periodic boundary conditions, i.e., upon leaving one face of the simulation volume, you re-enter in the opposite face. This can lead to molecules being split over the periodic boundary, which requires rectification before performing calculations. This project would involve defining wrapping and unwrapping functionality in the various AtomGroup methods which are based upon the position of particles, e.g., center of mass. Due to performance considerations, the functionality of these methods will also require translation into Cython.

Organization

Student

Ninad Bhat

Mentors

  • Oliver Beckstein
  • Richard Gowers
  • Micaela Matta
  • Jonathan Barnoud
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2019