Macromolecular Modelling on the Cray T3D

Abstract

The two basic methods of computational chemistry, namely electronic structure calculations (quantum mechanics, QM) and those based upon force fields (molecular mechanics, MM) are now widely used, in a routine fashion, to model many aspects of the structure and reactivity of macromolecular systems. Energy minimizations based upon quite simple representations of inter—atomic interactions via MM force fields can be used to predict the geometric structure of systems having many thousands of atoms, whilst their motion, particularly important in many biological problems can be followed using molecular dynamics (MD) simulations. These latter studies are particularly computationally intensive due to the quite long time scales that often need to be simulated.