This project aims to implement support for Molecular Dynamics in Avogadro.

Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles. In this project, we aim to provide support in Avogadro for reading MD trajectory files and analyzing the various aspects of the MD calculation like temporal evolution, particle movement characterization (eg. pair distribution functions) etc. Also, input generation and support for running MD calculations in common packages like OpenMM and GROMACS shall be focused upon in the later stages of the project.

Organization

Student

Adarsh Balasubramanian

Mentors

  • Marcus D. Hanwell
close

2018