Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aeqm_v1_0.tar.gz(12 Kbytes)|
|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.
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.
The current version only supports orthorhombic cells.
The Density Profile Tool is not a standalone program but a plug-in that enhances VMD's analysis features.
A contemporary PC completes the analysis of 500 frames of the example system discussed in the paper (35,000 atoms) in under 1 min.
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