{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/computing-1-d-atomic-densities-in","title":"Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD","arxiv_id":"1308.5873","date":"2013-08-27","proceeding":null,"authors":["Toni Giorgino"],"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.","url_abs":"https://arxiv.org/abs/1308.5873v1","url_pdf":"https://arxiv.org/pdf/1308.5873v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"computing-1-d-atomic-densities-in","repo_url":"https://github.com/giorginolab/vmd_density_profile","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"computing-1-d-atomic-densities-in","repo_url":"https://github.com/ClaireLoison/my_vmd_density_profile","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"computing-1-d-atomic-densities-in","repo_url":"https://github.com/tonigi/vmd_density_profile","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}