You can try using volmap plugin in VMD. It calculates spatial variation of properties (you can use mass as the property) using 3D grids. This data can be later used in combination with the molecule visuals to see areas of low mass density (voids).

http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node153.html

http://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/

Thank you. I will look into these.