Dear gromacs users, I am trying to pull a ligand out of a cavity of a membrane protein (along the Z axis). Problem is, that with every pull settings I have tried the ligand gets "stuck" on the protein's center of mass. How can I make it go all the was to the bulk water? It always gets stuck on the COM. And I've tried using both umbrella and constant force, so I'm getting the feeling that I'm missing something trivial.
Here's an example of one set of pull-parameters I tried: -------------------------------> pull = constant_force pull_geometry = distance pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = Ligand ;pull_rate1 = -0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 <------------------------------ Can anyone help enlighten me as to what I am doing wrong? Thanks, -Shay P.S. Using gromacs 4.0.7.
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