MDAnalysis provides a python framework to allow users to analyse Molecular Dynamics (MD) simulations. Umbrella Sampling (US) is an MD technique which involves performing a series of simulations in which a ‘reaction coordinate’ – such as distance between two molecules – is restrained to different values. Simulation data can be combined, usually using the WHAM method, to produce a ‘potential of mean force’ (PMF) profile that shows the energy landscape along the chosen coordinate. Several implementations of WHAM exist, but require input files of specific formats which may differ from that obtained directly from the simulation, dependent on the simulation engine used. Additionally, it would be convenient be able to calculate the PMF alongside analysis of the trajectory such as offered by MDAnalyisis. However, MDAnalysis does not yet have tools specifically for dealing with and analysing US simulations. This project aims to introduce capabilities for loading US simulation sets, including a generalised tool for loading auxiliary data files, and performing WHAM and other basic analysis.

Student

fiona

Mentors

  • Richard Gowers
  • Max Linke
  • Jonathan Barnoud
  • mnmelo
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2016