Faraday Discussion 169: Molecular Simulations and Visualization

7 - 9 May 2014, Nottingham, UK

By Phil Fowler, SSI Fellow and Postdoctoral researcher, Department of Biochemistry, University of Oxford

Highlights:

  1. How we visualise simulation data is vital and drives how we interpret and analyse the results.
  2. Technologies from gaming are starting to be used in biomolecular simulations.
  3. The use of GPUs to accelerate algorithms is continuing.

Event report:

The theme of the 169th Faraday Discussion was Molecular Simulations and Visualization. In my field we usually focus on the "science" and don't often get a chance to talk about new methods of visualizing the molecular trajectories produced by our simulations, so this was a rare opportunity. It turned out to be both interesting and inter-disciplinary, with talks ranging from computer games teaching students immunology to using the shapes generated by dancers to help fold proteins. From a software perspective, it was interesting to see how researchers were using open source gaming engines (Unity) and physics engines (bulletphysics) to not only build games but also create research software. For example cellPack is using bulletphysics to, for example, pack all the molecular components into the interior of a model of HIV.

There was also a talk by John Stone (UIUC, Urbana-Champaign) who is the developer of VMD, the most popular visualization package in the biomolecular simulation field. He showed how they have put a lot of effort into rewriting the code to make use of a GPU, if one is available, to in some cases accelerate some algorithms by a factor of 30. Finally, exaViz is a framework to handle in situ analysis of simulation data on high performance computers (HPC). This is becoming increasingly important because the existing approach of saving and retrieving all the simulation data from HPC is becoming unsustainable due to the quantities of data involved. Bruno Raffin showed how they have implemented exaViz with GROMACS, one of the most popular biomolecular molecular dynamics packages, and are able to handle trajectory formation and analysis in situ i.e. whilst the simulation is running. As this was a Faraday Discussion meeting all the participants were expected to have read all the papers beforehand and the majority of the time was devoted to a discussion, the results of which are published in the same volume of Faraday Discussions as the papers.