Dear GMXers, I'm trying to compute the PMF of a molecule along the centerline of a nanotube (the axial direction of the nanotube is parallel to the z axis). The nanotube is used as the reference group and the molecule as the pulling group.
pull_geometry = position pull_dim = Y Y Y pull_start = no pull_init1 = 0 0 1.2 pull_rate1 = 0.00 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 "pull_dim=Y Y Y" is used to make sure that the molecule is always close to the centerline of the nanotube. >From the output of "pullx.xvg", the COM positions in all three directions (i.e. x,y,z) are included. How to get the PMF only along z axis from here? Is it OK if I just take the corresponding z column and do g_wham directly? Thank you. Best, Yanbin
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