Google Summer of Code Students 2018

We are happy to anounce that MDAnalysis is hosting two GSoC students for NumFOCUS this year, Ayush Suhane (@ayushsuhane) on GitHub) and Davide Cruz (@davidercruz).

Ayush Suhane: Improve Distance Search Methods in MDAnalysis

Ayush Suhane

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 \(\mathcal{O}(N^2)\), 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 is a graduate student in Materials Engineering at UBC, Canada. He is working with Molecular dynamics simulations for his Master’s thesis. He wishes to contribute to the open source community by simplifying the complex analysis and visualization involved in MD. During GSoC, he aims to use the opportunity to learn from the already established open source contributors and continue the tradition by becoming an active member of the community. In his free time, he also likes to read fiction novels and play computer games.

Ayush will describe his progress on his blog.

Davide Cruz: Implementing on-the-fly coordinate transformations

Davide Cruz

Implement trajectory transformations on the MDAnalysis API, to be called on-the-fly by the user, eliminating the requirement for multiple intermediate steps of modifying and saving the trajectory, and giving users a more efficient and simple workflow for simulation data analysis.

Davide is currently on the last year of his PhD on Molecular Biosciences at ITQB-NOVA in Lisbon, Portugal. For his thesis he is using MDAnalysis to analyse the results of molecular dynamics simulationations and this GSoC project is an opportunity to contribute to the community. He expects to learn a lot about python and software development during this summer.

Davide will describe his progress on his blog.

Other NumFOCUS students

NumFOCUS is hosting 45 students this year for several of their supported and affiliated projects. You can find out about the other students here.