Time-averaged normal coordinate analysis of polymer particles and crystals

A common problem in the application of normal coordinate analysis to study low-frequency modes of large molecular systems is the occurrence of a large number of negative eigenvalues (unstable modes). By averaging the terms of the Hessian matrix over a short classical trajectory, the unstable modes w ere found to be completely eliminated for 6000 atom model polymer particles and crystals. The time-averaged matrices were made possible by an efficien t analytical formulation of the Cartesian second derivatives and diagonaliz ation was achieved using a sparse matrix solver (ARPACK). (C) 2000 Elsevier Science B.V. All rights reserved.