Dear Gmx Users, I run a simulation of a protein and 10 ligands. They all stacked on the protein surface. I extracted the coordinates of the somplex and I am doing Umbrella Sampling - I am trying to pull one of the ligand from my protein. My questions: Would you suggest restarining positions of the protein (and 9 other ligands?) when pulling my ligand? Would you restrained positions of the protein when running simulations in each window? How do you adjust the pulling constant force? Is there any rule or you just change it and observe?
Thank you, Steven
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