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Short helpfile for action S2CM
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The input trajectory can be in any of the following formats: 

            METHYL_ATOM - the methyl carbon atom of the residue (i). For more 
                          information on how to specify lists of atoms see \ref Group 
               NH_ATOMS - the hydrogen atom of the NH group of the residue (i) and 
                          carbonyl oxygen of the preceding residue (i-1). For more information 
                          on how to specify lists of atoms see \ref Group 
            HEAVY_ATOMS - the heavy atoms to be included in the calculation. For more 
                          information on how to specify lists of atoms see \ref Group 

The following arguments are compulsory: 

                  R_EFF - the effective distance, r_eff in the equation, given in nm. 
            PREFACTOR_A - the prefactor, a in the equation 
             EXPONENT_B - the exponent, b in the equation 
               OFFSET_C - the offset, c in the equation 
                    N_I - n_i in the equation 

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 
                 SERIAL - ( default=off ) Perform the calculation in serial - for 
                          debug purpose 
                  NLIST - ( default=off ) Use a neighbour list to speed up the 
                          calculation 
              NL_CUTOFF - The cutoff for the neighbour list 
              NL_STRIDE - The frequency with which we are updating the atoms in the 
                          neighbour list 
                R_SHIFT - shift all distances by given amount 


