Dear gmx-users Iwould like to calculate the PMF between two nanotubes covered with some molecules. To do that, one nanotube has to be held fixedly and another one is supposed to be moved as a rigid entity. To generate configurations, for fixed nanotube I used position restraints in all directions and for rigid nanotube, I used the combination of distance restraint plus position restraint in y and z direction ( x is myreaction coordinate) to keep the nanotube shape. My question is, after obtaining all configuration, can I use position restraint for both nanotubes in all directionsin umbrella sampling step or I should conduct this step in the same condition of generation of configuration step? I appreciate your time and help.
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