The surface area in MD simulations for particle is generally calculated by taking the position of the single atoms. Taking the center of the atom and the Van-der-waals radius. These Spheres intersect and contribute to the total surface are if they are the outmost and do not intersect.
There are two very good tools to calculate the surface area:
- msms:
http://mgl.scripps.edu/people/sanner/html/msms_man.html
Downloading the binaries: http://mgltools.scripps.edu/downloads
Java Script to test code: http://www.scripps.edu/~sanner/msms-jmol/
Tutorial: http://structbio.vanderbilt.edu/comp/soft/msms/tutorial.php
- vorlume:
http://cgal.inria.fr/abs/Vorlume/
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