VMD Density Profile Tool

The Density Profile Tool is a VMD [1] analysis plugin that computes 1-D projections of various atomic densities. The computation may be performed in a single frame, a trajectory, or averaged over multiple frames.

• Number density, i.e. average number of atoms per unit volume
• Mass density
• Charge density
• Electron density, i.e. average number of electrons.

[1] Visual Molecular Dynamics (VMD), http://www.ks.uiuc.edu/Research/vmd/

Author

Toni Giorgino
National Research Council of Italy (CNR)
toni.giorgino at cnr.it

Citation

Please cite this paper when publishing results obtained with the Density Profile Tool:

• Giorgino T. Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD. Computer Physics Communications. 2014 Jan;185(1):317–22. Available from doi:10.1016/j.cpc.2013.08.022 or preprint at arXiv:1308.5873

Installation

See instructions here.

Documentation

Further documentation is available in the doc subdirectory.

For an extensive description of the tool, together with the comparison with experimental data, see the Density Profile paper

Quickstart

Once correctly installed, a menu item should appear in VMD's Extensions menu, under "Extensions>Analysis>Density Profile Tool".

The plugin can be used interactively or via a scripting interface. See the included test script (example.tcl) for an example of in-script usage. The script

1. loads Klauda's equilibrated membranes (http://terpconnect.umd.edu/~jbklauda/research/download.html), POPC Bilayer (303.00K, NPT, 35ns, 72 lipids);
2. computes the mass density profile for water molecules, showing it as a table and a plot;
3. computes the electron density profile for the whole system, showing it as a plot.

Sample output for point 2.:

| Bin breaks coordinates: (z, Angstroms)
	| Density of water in each bin: (g/mol/A^3)
 -35.00	  0.00
 -34.00	  0.28
 -33.00	  0.65
 -32.00	  0.61
 -31.00	  0.62
 -30.00	  0.60
 -29.00	  0.62
 -28.00	  0.56
 -27.00	  0.56
 -26.00	  0.61
 -25.00	  0.55
[...]
  28.00	  0.58
  29.00	  0.64
  30.00	  0.56
  31.00	  0.57
  32.00	  0.60
  33.00	  0.25
  34.00	  0.00

License

Density Profile Plugin Copyright (C) 2012

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.