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

               RESIDUES - this command is used to specify the set of residues that 
                          could conceivably form part of the secondary structure. It is 
                          possible to use residues numbers as the various chains and residues 
                          should have been identified else using an instance of the \ref 
                          MOLINFO action. If you wish to use all the residues from all the 
                          chains in your system you can do so by specifying all. 
                          Alternatively, if you wish to use a subset of the residues you can specify 
                          the particular residues you are interested in as a list of 
                          numbers. Please be aware that to form secondary structure elements 
                          your chain must contain at least N residues, where N is 
                          dependent on the particular secondary structure you are interested 
                          in. As such if you define portions of the chain with fewer than 
                          N residues the code will crash. 

The following arguments are compulsory: 

                   TYPE - ( default=DRMSD ) the manner in which RMSD alignment is 
                          performed. Should be OPTIMAL, SIMPLE or DRMSD. For more details on the 
                          OPTIMAL and SIMPLE methods see \ref RMSD. For more details on the 
                          DRMSD method see \ref DRMSD. 
                    R_0 - ( default=0.08 ) The r_0 parameter of the switching 
                          function. 
                    D_0 - ( default=0.0 ) The d_0 parameter of the switching function 
                     NN - ( default=8 ) The n parameter of the switching function 
                     MM - ( default=12 ) The m parameter of the switching function 

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 
                VERBOSE - ( default=off ) write a more detailed output 
                 SERIAL - ( default=off ) do the calculation in serial. Do not use 
                          MPI 
                 LOWMEM - ( default=off ) lower the memory requirements 
                TIMINGS - ( default=off ) output information on the timings of the 
                          various parts of the calculation 
              LESS_THAN - calculate the number of variables less than a certain 
                          target value. 
                    MIN - calculate the minimum value. 
                ALT_MIN - calculate the minimum value. 
                 LOWEST - this flag allows you to recover the lowest of these 
                          variables. The final value can be referenced using 
                          <em>label</em>.lowest 
                HIGHEST - this flag allows you to recover the highest of these 
                          variables. The final value can be referenced using 
                          <em>label</em>.highest 


