We display the free volume by a surface-rendering technique borrowed from biomolecular simulations. They consist of a single PIB chain of 80 monomers interacting with its periodic images due to the cubic periodic boundary conditions. The equations of motion are integrated by the leap-frog algorithm with a time step of 2 fs. Into these samples eight oxygen molecules are inserted. No further equilibration is necessary.
All jumps have different characteristics.
This choice is, of course, arbitrary to some extent. Details of the forcefield will be given elsewhere. For the rendering of penetrant accessible surfaces a raw 3D mesh data is generated using the algorithm by Voorintholt et al. This method is very fast and convenient if one wants to look at the molecular surfaces for several different probe radii without the recalculation of the mesh data. This approach can be used to study outer molecular surfaces as well as cavities and channels inside molecules.