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

                  ATOMS - atoms for which we calculate the shadow RMSD. For more 
                          information on how to specify lists of atoms see \ref Group 

The following arguments are compulsory: 

                 UPDATE - stride for updating reference coordinates 

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 
              REFERENCE - ( default=off ) this is the reference replica 

