I understand it must be routine to perform these experiments, but due to my lack of much expertise in the field I have no other option but to ask here. I want to perform refolding kinetics of a protein (Go model) using gorex.pl module, but for that I need initial unfolded conformations. I can probably perform thermal heating at high temperature e.g. 500K to 550 K (go replica exchange limit) with 4 to 8 replicas to get good exchange. But I am not sure how to obtain different starting conformations. Probably different pdb's can be extracted after specific number of cycles. But how do I decide which ones to choose from. Or I will really appreciate if there is any other more recommended solution.