Diffusion Coefficient Tool (alpha)
Toni Giorgino — © Universitat Pompeu Fabra 2011
The Diffusion Coefficient Tool is an analysis plugin for VMD that computes one, two or three-dimensional MSD-based diffusion coefficients of a chosen molecular species.
This is alpha software. If you don't know how to compute the diffusion coefficient yourself, probably you won't be able to use this software. NO support or warranty is available whatsoever.
Usage
(Preliminary documentation)
The plugin is accessible from VMD in Extensions > Analysis > Diffusion Coefficient Tool. The profile is computed for the currently loaded trajectory in the top molecule. The atom selection must match one atom per diffusing molecule; MSD values will be averaged over the matched atoms.
Two buttons are provided to plot the MSD displacement and the Diffusion coefficient. The latter is computed with the Einstein relation as 1/2D MSD(t)/t, where D is the dimensionality of the system.
The Analysis interval boxes allow to specify a subsection of the trajectory to be used for the MSD calculation. Only displacements in the subspace spanned by the Diffusion along axes will be considered. In other words, if z is deselected, motions along that axes will be irrelevant for the calculation of MSD and D.
The results are given in Å2/ns. Conversion factors:
0.1 Å2/ns = 10-12 m2/s = 10-8 cm2/s = 1 μm2/s
1 cm²/s = 107 Ų/ns
1 m²/s = 1011 Ų/ns
1 μm²/s = 0.1 Ų/ns
1 Ų/ns = 10-7 cm²/s = 10-11 m²/s = 10 μm²/s
Upon completion, the location of a data file with the computed profiles will be printed on the console.
Warnings:
Don't draw premature conclusions. Computing converged diffusion coefficients is likely beyond your sampling capacity and patience, unless done for plenty of molecules (ie. solvent). Expect microseconds sampling.
- The trajectory must not be wrapped.
- A check is performed whether bonds exist between the selected atoms. This check may fail if wrong connectivity is inferred on molecule load;
Screenshot
Installation
Download the plugin and follow the instructions therein.
Licensing
By downloading the software you agree to comply with the terms of GPL version 2. The Tool may be described in a forthcoming publication. You are kindly requested check here if a citation is available when publishing results obtained with the tool.
Acknowledgments
Work partially supported by the Generalitat de Catalunya.