John Anderson

• Mchem (Hons) Chemistry (Industrial Training)
• Fast But Not Furious - Molecular Dynamics simulations and molecular docking calculations of protein complexes on a CPU/GPU system

Computational chemistry encompasses a variety of hardware and software that allows the modern chemist to find many qualities of a molecule quite reliably without ever entering a lab. Many of the tools developed thus far are still being developed and optimised to run on ever evolving hardware. Examples include Gromax which predicts molecular dynamics (motion of atoms within the molecule) for a molecule and DOCK6 which allows for prediction of the favourability of a molecule to bind to a site of another. Both of these, until recently, have not employed a large part of the modern computer, the GPU (Graphics Processing Unit). Gromax now supports the use of a GPU whereas DOCK6 still does not. It would therefore be valuable to examine how effective the use of various GPUs are and to find and test alternative programs to DOCK6 which do make use of the GPU.  

Funding source: Newcastle University

Supervisor: Dr. Agnieszka K. Bronowska