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

              UMEMBRANE - all the beads of the upper membrane.. For more information 
                          on how to specify lists of atoms see \ref Group 
              LMEMBRANE - all the beads of the lower membrane.. For more information 
                          on how to specify lists of atoms see \ref Group 
                  TAILS - all the tail beads of the system.. For more information on 
                          how to specify lists of atoms see \ref Group 
                 WATERS - all the water beads of the system.. For more information on 
                          how to specify lists of atoms see \ref Group 
       PHOSPHATEOXYGENS - all the lipid phosphateoxygens beads of the system.. For 
                          more information on how to specify lists of atoms see \ref Group 

The following arguments are compulsory: 

                  NSMEM - the number of slices of the membrane fusion cylinder. 
                     NS - the number of slices of the membrane-spanning cylinder in 
                          such a way that when the bilayers are flat and parallel the CV 
                          is equal to 0.2. 

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 
                  DSMEM - ( default=0.1 ) thickness of the slices of the membrane 
                          fusion cylinder. 
                   HMEM - ( default=0.25 ) parameter of the step function θ(x,h) for 
                          the membrane fusion. 
                     DS - ( default=0.25 ) thickness of the slices of the 
                          membrane-spanning cylinder. 
                    HCH - ( default=0.25 ) parameter of the step function θ(x,h) for 
                          the CV. 
                   RCYL - ( default=0.8 ) the radius of the membrane-spanning 
                          cylinder. 
                   ZETA - ( default=0.75 ) parameter of the switch function ψ(x,ζ). 
      ONEOVERS2C2CUTOFF - ( default=500 ) cut off large values for the derivative of 
                          the atan2 function to avoid violate energy. 
                   XCYL - X coordinate of the fixed cylinder, if not present this 
                          will be calculated. 
                   YCYL - X coordinate of the fixed cylinder, if not present this 
                          will be calculated. 


