Transforming molecular biology research through extreme acceleration of AMBER molecular dynamics simulations: sampling for the 99%

Abstract

This talk will cover recent developments in the acceleration of Molecular Dynamics Simulations using NVIDIA Graphics Processing units with the AMBER software package. In particular it will focus on recent algorithmic improvements aimed at accelerating the rate at which phase space is sampled. A recent success has been the reproduction and extension of key results from the DE Shaw 1 millisecond Anton MD simulation of BPTI (Science, Vol. 330 no. 6002 pp. 341-346) with just 2.5 days of dihedral boosted AMD sampling on a single GPU workstation, (Pierce L, Walker R. C. et al. JCTC, 2012 in review). These results show that with careful algorithm design it is possible to obtain sampling of rare biologically relevant events that occur on the millisecond timescale using just a single $500 GTX580 Graphics Card and a desktop workstation. Additional developments highlighted will include the acceleration of AMBER MD simulations using graphics processing units including Amazon EC2 and Microsoft Azure Cloud based automated ensemble calculations, a new precision model optimized for the upcoming Kepler architecture (Walker R. C. et al, JCP, 2012, in prep) as well as approaches for running large scale multi-dimensional GPU accelerated replica exchange calculations on Keeneland and BlueWaters.