Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD

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. Program summaryProgram title: Density Profile ToolCatalogue identifier: AEQM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQM_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: yesNo. of lines in distributed program, including test data, etc.: 1742No. of bytes in distributed program, including test data, etc.: 12764Distribution format: tar.gzProgramming language: TCL/TK.Computer: Any, with or without graphical display.Operating system: Linux/Unix, OSX, Windows.RAM: VMD should be able to hold the trajectory in memory.Classification: 3, 23.External routines: VMD (version 1.9 or higher) (http://www.ks.uiuc.edu/Research/vmd/).Nature of problem:Compute and visualize one-dimensional density profiles of molecular dynamics trajectories in the VMD environment, either interactively or programmatically.Solution method:Density profiles are computed by binning the simulation space into slabs of finite thickness. A graphical user interface allows the choice of the atomic property (number, mass, charge, electrons) and the details of the binning.Restrictions:The current version only supports orthorhombic cells.Unusual features:The Density Profile Tool is not a standalone program but a plug-in that enhances VMD’s analysis features.Running time:A contemporary PC completes the analysis of 500 frames of the example system discussed in the paper (35,000 atoms) in under 1 min.