Dear Chris, Thank you for your reply. My protein is very stable.
I simulated it in 300ns in 300K before but there was almost no change. That's why I want to do denaturation now. I want to start a new simulation on the protein which is unfolded. And I'll read the paper you told me. Thank you. But I don't understand what you recommend me to do. You use 3000K on your protein and the protein unfolded. I use 600K on my protein but the system explode(box become very big and protein locate at corner). I saw the second way on this web, http://manual.gromacs.org/online/protunf.html But it also useless to me. And in my mdp I use thermostat and barostat, which means my system is NPT. Does anything wrong in my methods? Sincerely yours, Hsin-Lin
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