  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.
