The use of animated difference matrices for analysing protein molecular dynamics simulation data

Abstract

A method for analysing molecular dynamics data is described which uses animation on a calligraphic system. Each conformation from the dynamics experiment is represented by a 'frame' of an interactive movie. The frames show upper triangles of distance matrices calculated from the conformations. Distance matrices enable researchers to recognise cooperative motions of the atoms. Difference distance matrices, which are calculated by subtracting the corresponding elements of a distance matrix from those in the previous one, are also used to analyse the motions. In this paper the technique is explained and an example is given where these tools are being used to analyse results from a dynamics simulation of a polypeptide. © 1983.