Extraction of the energetics of selected types of motion from molecular dynamics trajectories by filtering.

A novel method for analyzing molecular dynamics trajectories has been developed which enables the study of selected motions and the corresponding energetics. In particular, it is possible to filter out the high-frequency motions and focus on the structural and energetic features of low-frequency collective motions. The trajectories of the properties of interest are Fourier transformed to the frequency domain, a filtering function is applied, and then an inverse transformation back to the time domain yields the filtered trajectory. The method is demonstrated for harmonic fluctuations and conformational transitions of acetamide and N-acetylalanine N-methylamide, as models for peptides and proteins.