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

Toni Giorgino
8/27/2013
physics.comp-phphysics.bio-phq-bio.BM

Official code: giorginolab/vmd_density_profile (39 stars, last commit 2023-05-08).

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.

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Code Implementations(1)

giorginolab/vmd_density_profileOfficial100%

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

3913Tcl, MakefileJun 11, 20143 years ago

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Cite this paper

@article{giorgino2013computing,
  title  = {Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD},
  author = {Toni Giorgino},
  year   = {2013},
  eprint = {1308.5873},
  archivePrefix = {arXiv},
  url    = {https://arxiv.org/abs/1308.5873}
}

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