Massively-Parallel Molecular Dynamics Simulations on New York Blue.
Molecular simulation provides a powerful tool to probe biochemical
function, and tera-to-peta Flop computational resources allow for larger
systems and timescales to be explored. In this talk, we will discuss
molecular simulation on BG/L with the NAMD software package. A detailed
description of how large-scale explicit solvent simulations have been
set up and run will be given. The key bottlenecks in parallel
performance of molecular simulations will be discussed, and scalability
of differently sized systems on BG/L will be presented. Examples will
be given from initial results on the dynamics and energetics of key
structural states of the heterotrimeric G-proteins.