Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined). I would like to run NPT before running umbrella sampling simulations. As far I see Justin in his tutorial NPT and umbrella sampling mdp files looks the same which means you did not restrain whole protein in your system during NPT? Why? Shall rund NPT withou restraining protein and ligand before umbrella sampling in each window?
Thank you, Steven
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