Hello, I am studying the diffusion of a small molecule through a cyclic peptide based nanotube using pull code, here is my code for pulling,
pull = umbrella pull_geometry = position pull_vec1 = 0 0 1 pull_start = yes pull_ngroups = 1 pull_group0 = Protein pull_group1 = FLU pull_rate1 = 0.005 pull_k1 = 1000 my reference group is a nanotube and pulling group is a small molecule. In this study, should I have to apply position restraint for the protein molecules? Regards, Vijay.
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