[gmx-users] Question about umbrella sampling through a nanotube

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

[gmx-users] Question about umbrella sampling through a nanotube

Unfortunately, I don't think that there is any way to use this data (and only this data) to derive the PMF along z. The way that you did your US, the PMF along z is convoluted with xy motion. You can get the PMF along the reaction coordinate that you actually used (XYZ) using standard WHAM