VMD Density Profile Tool (beta)

Toni Giorgino — © Universitat Pompeu Fabra 2011

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

Atomic density, i.e. average number of atoms
Mass density
Charge density
Electron density, i.e. average number of electrons.

Usage

(Preliminary documentation)

The plugin is accessible from VMD in Extensions > Analysis > Density Profile Tool. The profile is computed for the current frame in the top molecule. For mass and charge computation, a topology file must be loaded.

When dealing with a trajectory, the behaviour depends on the average check box: if selected, density profiles for all of the frames will be plotted; otherwise, the average plus or minus the standard deviation will be displayed (but see the note below).

If periodic cell information is available in the molecule (e.g. as set in pbctools), the density will be properly normalized with respect to the volume. Otherwise, it will be simply projected along a linear axis. Note that you will still need to wrap atoms yourself.

Assuming that periodic box information is available, results are given in the following units:

Atomic density: atoms/Å³
Mass density: amu/Å³
Charge density: e/Å³
Electron density: electrons/Å³

For electron density calculations, the atomic number is inferred from the first character in VMD's name, type, or element atom attributes (as selected in the GUI). The correct choice depends on how the topology was prepared. (If necessary, you can rename atoms inside VMD.)

Unit conversions:

in moles per liter, multiply by 1661 Å³ mol/l (or the value appropriate at your temperature)
1 amu/Å³ = 1.66 g/cm³

Example

See attached screenshot for the water density profile around a POPC membrane. Note how the water density in bulk goes to the macroscopic value of 18/30 amu/A³.

Limitations

atoms are assumed as point-like
only orthorombic cells are supported
periodic boundary conditions are assumed to be constant over the trajectory, so NPT is not supported
due to a temporary bug, averaging requires step to be 1

Screenshot

Installation

Download the plugin source and follow the instructions therein.

Licensing

This is beta software. By downloading the software you agree to comply with the terms of GPL version 2. The Tool will be described in a forthcoming publication which you are kindly requested to cite. Please check in this page the updated citation, currently being:

Toni Giorgino, Computing 1D atomic densities in macromolecular simulations: the Density Profile Tool for VMD, http://multiscalelab.org/utilities/DensityProfileTool (accessed xxx, xxx 2011).

Acknowledgments

Work partially supported by the Generalitat de Catalunya.