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

Published: 1 January 2014| Version 1 | DOI: 10.17632/9n2kdsf2t9.1
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 w... Title of program: Density Profile Tool Catalogue Id: AEQM_v1_0 Nature of problem Compute and visualize one-dimensional density profiles of molecular dynamics trajectories in the VMD environment, either interactively or programmatically. Versions of this program held in the CPC repository in Mendeley Data AEQM_v1_0; Density Profile Tool; 10.1016/j.cpc.2013.08.022 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)



Molecular Biology, Statistical Physics, Biological Sciences, Computational Physics, Thermodynamics