Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD

TL;DR

The paper introduces the Density Profile Tool, a VMD plugin that enables interactive computation and visualization of 1-D atomic density profiles in molecular simulations, aiding structural analysis.

Contribution

It presents a new software tool integrated with VMD for calculating and visualizing atomic density profiles from molecular simulation data.

Findings

Effective measurement of membrane thickness and structural element locations.

Comparison of density profiles with X-ray diffraction data.

Application to realistic all-atom bilayer models.

Abstract

Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to analyze simulated trajectories, either interactively or via scripts, to derive quantities of interest and provide insight for further experiments. This paper presents the Density Profile Tool, a package that enhances the Visual Molecular Dynamics environment with the ability to interactively compute and visualize 1-D projections of various density functions of molecular models. We describe how the plugin is used to perform computations both via a graphical interface and programmatically. Results are presented for realistic examples, all-atom bilayer models, showing how mass and electron densities readily provide measurements such as membrane thickness, location of structural elements, and how they compare to X-ray diffraction experiments.