ExTASY - the Extensible Toolkit for Advanced Sampling and analYsis - provides high-performance software products to enhance our ability to understand the behaviour and function of complex macromolecules such as proteins, DNA, and other bio-molecules through sampling with molecular dynamics (MD) simulations.
In theory, molecular dynamics is a good way to sample the conformational space accessible to a molecular system, but in practice the computational time and expense required to get adequate sampling to make reliable predictions of properties or behaviour is frequently out of reach, even with state-of-the art simulation software, HPC, and purpose-built hardware.
The ExTASY project has developed tools for a three-pronged attack on the problem:
More sampling through more simulations:
Support for high-performance high-throughput execution of ensembles of MD calculations. This means managing hundreds or thousands of coupled parallel jobs, each of which may run on hundreds of CPU cores as well as orchestrating associated 'big data' movement and interfacing with analysis tools in a heterogeneous execution environment spanning UK (e.g. ARCHER) and US (XSEDE) compute resources.
Better sampling through biased simulations:
Developing novel analysis tools to allow on-the-fly control of the simulations to bias sampling (in a mathematically rigourous way) towards the rare events or long-timescale motions of a system.
Faster sampling through better algorithms:
Providing a flexible and portable interface to existing highly-tuned MD programs coupled with new algorithms for MD integration with ultra-large time steps.
Software tools: MIST
Achieving these three objectives together within a single framework and interoperable set of tools will truly make a step change in our ability to compute and understand the dynamics of complex macromolecular systems.