AmberGPUMDSimulation_1.0

The need for efficient and reproducible computational tools in theoretical biophysics has continued to grow. With the drive towards high throughput simulations involving larger numbers of simulation systems performed at longer, more biologically relevant timescales, the need for new computational methods that facilitate molecular dynamics simulations gains more importance. We developed a flexible and robust workflow to perform MD simulations. This workflow capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust simulation engine, which one can reliably carry out MD simulations. Additionally, this workflow reduces user interaction time by automating repetitive processes, and facilitates access to GPU clusters, whose high performance processing power makes simulations of large numerical scale possible. The flexibility of the Kepler workflow comes from its ability to access a range of computing resources.