Dear gromacs users, I am studying gromacs umbralla sampling. I want to pull a lingand out of its binding pocket in a protein. By observing the ligand-protein complex, I think I should pull the ligand along a direction which is not parallel to the x, y or z axis so as to prevent the ligand colliding with the atoms around the the pocket. So I have to define a box whose long axis is parallel to the pulling direction. Could anyone explain to me that how to define the box? Thanks in advance! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences
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