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Short helpfile for action FUNNEL_PS
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The input trajectory can be in any of the following formats: 

                 LIGAND - This MUST be a single atom, normally the COM of the ligand. 
                          For more information on how to specify lists of atoms see \ref 
                          Group 
                 ANCHOR - Closest protein atom to the ligand, picked to avoid pbc 
                          problems during the simulation. For more information on how to 
                          specify lists of atoms see \ref Group 

The following arguments are compulsory: 

              REFERENCE - a file in pdb format containing the structure you would 
                          like to align. 
                 POINTS - 6 values defining x, y, and z of the 2 points used to 
                          construct the line. The order should be A_x,A_y,A_z,B_x,B_y,B_z. 

In addition you may use the following options: 

  NUMERICAL_DERIVATIVES - ( default=off ) calculate the derivatives for these 
                          quantities numerically 
                  NOPBC - ( default=off ) ignore the periodic boundary conditions 
                          when calculating distances 
           SQUARED-ROOT - ( default=off ) Used to initialize the creation of the 
                          alignment variable 

