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Manuscript Title: Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD
Authors: Toni Giorgino
Program title: Density Profile Tool
Catalogue identifier: AEQM_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 185(2014)317
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.
Keywords: Electron density, Projection, Bilayer, Cholesterol, Lipid, Phospholipid, Membrane, Trajectory, Structural biology, Graphical user interface, GUI, Computational, Molecular graphics.
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.