FOCUS: a program for analyzing molecular dynamics simulations, featuring digital signal-processing techniques.

Abstract

FOCUS is a program for analyzing molecular dynamics simulations. It enables the researcher to monitor structural and energetic properties during the trajectory, and to calculate the corresponding statistical averages, correlation functions and Fourier transforms. In addition to these conventional methods, the program also utilizes novel methods based on digital signal-processing techniques to characterize the various motions. The characteristic frequencies in the system are revealed by the frequency distribution function g(v), which is calculated from the Fourier transform of the atomic coordinates. A filtering technique is employed to remove uninteresting motion (e.g., high-frequency bond stretching) while retaining and focusing on important motion (e.g., low-frequency conformational motion). The filtering technique enables fast display of slow events without getting a blurry or jittery picture due to the high-frequency motions. Another new way for analyzing the motion is by extracting "characteristic modes" and associated frequencies. This yields a pictorial description of the oscillatory motions in a manner analogous to normal mode analysis.