MDanalysis (MDA) is a powerful open-source package for exploring and performing calculations on molecular dynamics trajectories. Despite MDAs broad utility, especially for biomolecular simulations, it does not implement many common operations for studying ion solvation. I propose adding a robust and cohesive set of methods for solvation analysis that would be widely useful in both biomolecular and battery electrolyte simulations. The core of the solvation module will be a cohesive set of functions for easily working with ionic solvation shells. Using that core functionality, I will implement several analysis methods for analyzing ion pairing, ion speciation, residence times, and shell association and dissociation.

Organization

Student

orion cohen

Mentors

  • Irfan Alibay
  • Richard Gowers
  • Hugo MacDermott-Opeskin
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2021