Monday, October 24, 20163:00 PM - 4:00 PMCNLS Conference Room (TA-3, Bldg 1690)|
Pushing the envelop in Molecular Dynamics of Biological Systems: Speedups and New Ensembles
Adrian RoitbergUniversity of Florida
I will present some of our recent work on accelerating and adding features to the Suite of programs AMBER. In particular, I will describe the work on GPU coding, touching on issues of precision and hardware/software co-design. I will also show how we can treat pH as a thermodynamic variable in simulations, which enables us to sample protonation space properly and efficiently. Coupling of these methods with replica exchange ideas, allows to great computational scaling with significant gains in sampling efficiency.
Host: Angel E. Garcia