Hi, I try to pull the small molecule from the bulk solution to the surface by the Constraint function. However, it seems that it does not work well.
Here my part of run parameters about the Constraint in my mdp file ############################## constraints = all-bonds; hbonds; all-bonds constraint-algorithm = Lincs pull = constraint pull_geometry = distance pull_dim = N N Y pull_ngroups = 1 pull_group0 = Surface pull_group1 = Protein pull_nstxout = 1000 pull_nstfout = 1000 pull_rate1 = -0.001 pull_init1 = 1.73331 ########################## Based my understanding, the pull_rate1 is about -0.001/ps. That means in the pullx.xvg file, the distance shoud be as follows (only the z-distance shown, time step is 1fs.) 1.73331 1.72231 1.72131 1.72031 . . However, in my simulation, the results from the simulation is as follow: 1.73331 1.71154 1.75043 1.73213 1.78065 1.79769 1.84298 1.87008 It seems some force has been imposed on the pull molecules. But in the pullf.xvg the force is ZERO. I used the latest gromacs version, But for the gromacs4.0 it works very well (works as what I think). Can someone help me about the issue? Thanks a lot Jerry
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