[gmx-users] diffusion through nanotube

[Vijayaraj]

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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