Implementation and characterization of protein folding on a desktop computational grid: is CHARMM a suitable candidate for the united devices MetaProcessor?

Abstract

CHARMM is a popular molecular dynamics code for computational biology. For many CHARMM applications such as protein folding, desktop grids could become viable alternatives to clusters of PCs. In this technical report, we present a prototype and discuss the viability of a protein folding application with CHARMM on the United Devices MetaProcessor, a platform for widely distributed computing. We identify the algorithmic approach of protein folding as a hybrid search algorithm with best-first, depth-first and breadth-first components and address the issues of task scheduling and fault tolerance. The performance evaluation of our system indicates that the calculation is robust against the heterogeneity of compute nodes and limited communication capabilities typically found in desktop grids. We show that there is an interesting tradeoff between accuracy and task parallelism resulting in optimal work-pool size for a given platform and a given simulation. Surprisingly the platform heterogeneity of a desktop grid positively affects the quality of protein folding simulations. Protein folding calculations with CHARMM turn out to be well suitable for desktop grids like e.g. the United Devices MetaProcessor. Our software system can make a large amount of nearly free compute cycles available to computational biologists.