Full-atom simulation of biomolecules using molecular dynamics on ultrascalable parallel computers

Author: Xin Chen (SUNY Stony Brook; Grad student)

Abstract

We have developed a "molecular dynamics on a chip" (MDoC) package for ultra scalable supercomputers with up to hundreds of thousands of processors such as IBM's Blue Gene/L and Columbia University's QCDOC. These machines, connected by cellular networks on 3D and 6D topologies, are capable of 360 Tflops.

Simulating large proteins for microsecond physical time will offer us great insights to the structures of such proteins but it has been a serious challenge to most computational biologists to achieve such time scale. Our package is estimated to achieve one microsecond for a protein with 10,000-atoms on 8,000-processor QCDOC within two weeks of running time. The core of our molecular dynamics is the technique in computing the electrostatic forces by FFT and all-to-all communication on such massive systems.

We will also present the preliminary results of analyzing the conformational structure changes of a biotoxin Botulinum with more than 170,000 atoms including explicit solvents at pH4.7 and pH7.0 and temperatures T=37C and 55C up to sub-microseconds.