Paper Citing NAMD - Abstract
Schulz, Roland; Lindner, Benjamin; Petridis, Loukas; Smith, Jeremy C.
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2798-2808, OCT 2009
A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors, other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million-atom biological systems scale well up to similar to 30k cores, producing similar to 30 ns/day, Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.
