Morphological Image Analysis
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- Last Updated: Thursday, 22 August 2013 10:01
Morphological Image Analysis Tool
When analyzing computer simulations of mixtures of lipids and water, the questions to be answered are often of a morphological nature. They can deal with global properties, like the kind of phase that is adopted or the presence or absence of certain key features like a pore or stalk, or with local properties, like the local curvature present at a particular part of the lipid/water interface. While in principle all of the information relating to the global and local morphological properties of a system can be obtained from the set of atomic coordinates generated by a computer simulation, the extraction of this information is a tedious task that usually involves using a visualization program and performing the analysis by eye. Here we present a tool that employs the technique of morphological image analysis (MIA) to automatically extract the global morphology—as given by Minkowski functionals—from a set of atomic coordinates, and creates an image of the system onto which the local curvatures are mapped as a color code. The implementation is intended for the analysis of mixtures of lipids and water obtained from molecular dynamics simulations, but is also in principle applicable to all kinds of coordinates that describe binary mixtures, and is independent of the model and the method used to generate the coordinates.
Details of the method are published in:
M. Fuhrmans, S.J. Marrink, A tool for the morphological analysis of mixtures of lipids and water in computer simulations, J. Mol. Mod. 17:1755-1766, 2011. open access
The required c programs can be downloaded here: MIA-source
A description how to use the package: MIA.pdf
For questions please contact Marc Fuhrmans (This email address is being protected from spambots. You need JavaScript enabled to view it.)