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 summary Program title: Density Profile Tool Catalogue identifier: AEQM_v1_0 Program summary URL: http: cpc.cs.qub.ac.uk summaries AEQM_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 1742 No. of bytes in distributed program, including test data, etc.: 12764 Distribution format: tar.gz Programming 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.
Other analysis packages contain command-line tools to perform density profile computations similar to the one described here. GROMACS' distribution, for example, provides +g_density+, a stand-alone executable meant to be used from the command-line or in shell scripts @cite_0 . This approach has the advantage of not being tied to a specific graphical or scripting environment; however, it can be limiting in three respects: first, a GUI may be desirable for quick one-off computations; second, binaries mostly require GROMACS-specific file formats and topologies; finally, performing computations in shell scripts implies a programming model in which text files are used to store intermediate results -- a model which is more cumbersome than manipulating variables, the route afforded by conventional programming languages like TCL or Python.
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Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of a...