Surface Area Calculations for MD

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/

Periodic table on the internet

Sometimes you look for chemical properties of materials.
A quite good periodic table can be found here:
http://www.webelements.com/

For Minerals this homepage can be a valuable resource:
http://www.mindat.org/

If you are looking for material properties, Springer Materials might also be a good resource.
http://www.springermaterials.com/navigation/

Graphical Plotting

Hi since SigmaPlot costs way to much for a student I started to look for different programms. For me the best so far was to use pgfplot for Latex.

Here is a nice tutorial for it:
www.tug.org/TUGboat/tb31-1/tb97wright-pgfplots.pdf 

The manual can be found here