Gridifying the TINKER conformer generator application for gLite grid

Abstract

Grid Computing provides an efficient way for parallelizing and gridifying computationally and data intensive applications of various research fields. One of these application areas is molecular dynamics. In this paper we examine a biochemical application that generates conformers by unconstrained molecular dynamics at high temperature to overcome conformational bias then finishes each conformer by simulated annealing and energy minimization to obtain reliable structures. We provide a general way for turning biochemical applications into Grid workflows that can be executed by Grid portals exploiting the computational power of available production Grids. First we describe the gridification process, then provide experimental results that show the achieved speed-up of the ported application. © 2011 Springer-Verlag Berlin Heidelberg.