TRAJAN - A TOOL FOR ANALYZING TRAJECTORIES FROM MOLECULAR SIMULATIONS

Molecular dynamics simulations of biological systems are notoriously d ifficult to analyze because of the complexity of the information that they contain. We describe a new method for analyzing trajectories from simulations in order to extract important features of the motion. The trajectory of each atom is partitioned into conformation wells, in ea ch of which its motion is assumed to be predominantly harmonic oscilla tion around an average position. Thus each atom moves anharmonically t hrough a sequence of-wells during the trajectory. The movement of atom s between wells, their ellipsoids of motion within each well, and corr elations in the motion of atoms are quantified and can be visualized w ith molecular graphics. The TRAJAN analysis procedure is applicable to trajectories from equilibrium and nonequilibrium simulations and is n ot restricted to molecular dynamics simulations. Its application is de monstrated for a range of model systems.