QM/MM Molecular DynamicsAdrian Roitberg, University of Florida; Dave Case, The Scripps Research Institute
This SAC aims to accelerate semi-empirical and DFTB QM/MM techniques that were recently added to the AMBER molecular dynamics code in order to enable nano-second long or greater QM/MM molecular dynamics simulations to be run. This involves the development of shared memory and distributed matrix diagonalization routines that are optimized for the small matrices found in semi-empirical QM/MM calculations. This SAC effort also looks to enable explicit solvent QM/MM calculations to be run on proteins with a pure QM solute. This will allow investigations of protein reactivity and protein folding without the need for boundary approximations that plague current QM/MM approaches. Ultimately this work will benefit the thousands of scientists that use the AMBER software.