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

                  ATOMS - The list of molecules for which you would like to calculate 
                          the contact matrix. The molecules involved must have an 
                          orientation so your list will be a list of the labels of \ref mcolv or 
                          \ref multicolvarfunction as PLUMED calculates the orientations 
                          of molecules within these operations. Please note also that 
                          the majority of \ref mcolv and \ref multicolvarfunction do not 
                          calculate a molecular orientation.. For more information on how to 
                          specify lists of atoms see \ref Group 
                 ATOMSA - The list of molecules that you would like to use for the 
                          rows of the contact matrix. The molecules involved must have an 
                          orientation so your list will be a list of the labels of \ref mcolv or 
                          \ref multicolvarfunction as PLUMED calculates the orientations 
                          of molecules within these operations. Please note also that 
                          the majority of \ref mcolv and \ref multicolvarfunction do not 
                          calculate a molecular orientation. 
                 ATOMSB - The list of molecules that you would like to use for the 
                          columns of the contact matrix. The molecules involved must have an 
                          orientation so your list will be a list of the labels of \ref mcolv or 
                          \ref multicolvarfunction as PLUMED calculates the orientations 
                          of molecules within these operations. Please note also that 
                          the majority of \ref mcolv and \ref multicolvarfunction do not 
                          calculate a molecular orientation. 

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... 
     ORIENTATION_SWITCH - A switching function that transforms the dot product of the 
                          input vectors. You can use multiple instances of this keyword 
                          i.e. ORIENTATION_SWITCH1, ORIENTATION_SWITCH2, 
                          ORIENTATION_SWITCH3... 


