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

                  ATOMS - The list of atoms for which you would like to calculate the 
                          contact matrix. The atoms involved must be specified as a list of 
                          labels of \ref mcolv or labels of a \ref multicolvarfunction 
                          actions. If you would just like to use the atomic positions you can 
                          use a \ref DENSITY command to specify a group of atoms. 
                          Specifying your atomic positions using labels of other \ref mcolv or 
                          \ref multicolvarfunction commands is useful, however, as you can 
                          then exploit a much wider variety of functions of the contact 
                          matrix as described in \ref contactmatrix. For more information on 
                          how to specify lists of atoms see \ref Group 

The following options are available

  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 ) do the calculation in serial. Do not use 
                          MPI 
                TIMINGS - ( default=off ) output information on the timings of the 
                          various parts of the calculation 
                HIGHMEM - ( default=off ) use a more memory intensive version of this 
                          collective variable 
                 SWITCH - This keyword is used if you want to employ an alternative 
                          to the continuous switching function defined above. The 
                          following provides information on the \ref switchingfunction that are 
                          available. You can use multiple instances of this keyword i.e. 
                          SWITCH1, SWITCH2, SWITCH3... 


