Molecular simulations without capping n- and c-terminus of polypeptide
Interesting question. I have to admit, that I haven't really come across it, but for the moment it seems to me that this mechanism is used mainly to protect short alpha helices and stabilize them. 
See this articles: "Helix stop signals in proteins and peptides: the capping box." and this one: "Helix capping."
A lot of research is done in combination with actin filaments, where the capping plays an important role in stabilizing the filament strands - either prohibiting the addition of new monomers and on the other hand preventing the removal of elements from the polymer strand. 
This review gives an overview:"F-actin capping proteins."
This research article might also be interesting when doing simulations:"N- and C-capping preferences for all 20 amino acids in alpha-helical peptides." As always, if you have some problems with access to the articles, let me know.