With the capability of multiple MD codes to easily handle milions of atoms, a major roadblock to analysis of this vast amount of data corresponding to positions of each atoms at every timestep is the time to evaluate pairwise distance between multiple atoms. Almost every operation requires the distance between the pair of atoms, fast calculation of pairwise distance is of utmost importance. Multiple basic analysis functions like Radial Distribution Function, Contact Matrices, depepend very heavily on fast distance evaluations. Apart from naive approach for pairwise calculations which scale as O(N^2), other forms of data structures like KDTree, Octree are sugested for faster calulations based on the requirements. Based on the MDAnalysis, two use cases are identified as highly used in majority of the analysis algorithms. The goal of the project is to identify the data structure based on the requirements of the use case and implement in the MDAnalysis library along with clear documentations and test cases.



Ayush Suhane


  • Richard Gowers
  • Jonathan Barnoud