Dear Gmx Users, I am setting up my simulations of carbon tube with protein. I solvated my system, added ions and I would like to run EM of my system. My carbons of the tube in MD will be restrained. In this case should I run EM of my protein in water (and with ions) separately and the copy coordinates and then process with NVT and NPT or run EM with restrained nanotubes of my system directly?
Thank you, Steven
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