MolDyn – Molecular Dynamics

Veselin Dikov, Niko Manopulo, Darya Popiv, Ilya Saverchenko, Levi Valgaerts

Snapshot of a MollDyn simulation Snapshot of a molecular dynamics simulation

MolDyn was a team project of five students of the CSE-branch of the BGCE.

The project task was to design and implement, from scratch, a simulation package for molecular dynamics. The final code was required to include the following features:

  • modelling of molecules as rigid bodies interacting on collisions due to a Lennard-Jones 6-12-potential;
  • O(n) computational effort in all simulation steps, where n is the number of simulated molecules;
  • parallelisation based on a partitioning of the force-matrix to support the simulation of large problems;
  • embedding the code into an easy-to-use graphical interface for computational steering and visualisation of the results.

Within the project team, students took over specific roles (team leader, quality manager, etc.) in the software engineering process, in order to exercise project management and skills skills in addition to the scientific challenges.