TRAJAN: A Tool to Analyze Trajectories from Molecular Simulations

ABSTRACT:
Molecular dynamics simulations of biological systems are notoriously difficult to analyze because of the complexity of the information that they contain. We describe a new method to analyse trajectories from simulations in order to extract important features of the motion. The trajectory of each atom is partitioned into conformation wells in each of which its motion is assumed to be predominantly harmonic oscillation around an average position. Thus each atom moves anharmonically through a sequence of wells during the trajectory. The movement of atoms between wells, their ellipsoids of motion within each well and correlations in the motion of atoms are quantified and can be visualised with molecular graphics. The TRAJAN analysis procedure is applicable to trajectories from equilibrium and non-equilibrium simulations and is not restricted to molecular dynamics simulations. Its application is demonstrated for a range of model systems.