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Short helpfile for action RMSD
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The following arguments are compulsory: 

              REFERENCE - a file in pdb format containing the reference structure and 
                          the atoms involved in the CV 
                   TYPE - ( default=SIMPLE ) the manner in which RMSD alignment is 
                          performed. Should be OPTIMAL or SIMPLE. 
                 NUMBER - ( default=0 ) if there are multiple structures in the pdb 
                          file you can specify that you want the RMSD from a specific 
                          structure by specifying its place in the file here. If NUMBER=0 then 
                          the RMSD from all structures are computed 

In addition you may use the following options: 

                SQUARED - ( default=off ) This should be setted if you want MSD 
                          instead of RMSD 
                  NOPBC - ( default=off ) ignore the periodic boundary conditions 
                          when calculating distances 
  NUMERICAL_DERIVATIVES - ( default=off ) calculate the derivatives for these 
                          quantities numerically 
           DISPLACEMENT - ( default=off ) Calculate the vector of displacements 
                          instead of the length of this vector 

