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

                  SITES - The list of atoms which can be part of a hydrogen bond. 
                          When this command is used the set of atoms that can donate a 
                          hydrogen bond is assumed to be the same as the set of atoms that can 
                          form hydrogen bonds. 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 
                 DONORS - The list of atoms which can donate a hydrogen bond. 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 
              ACCEPTORS - The list of atoms which can accept a hydrogen bond. 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 
              HYDROGENS - The list of hydrogen atoms that can form part of a hydrogen 
                          bond. The atoms must be specified using a comma separated list, 
                          an index range or by using a \ref GROUP. For more information 
                          on how to specify lists of atoms see \ref Group 

The following arguments are compulsory: 

               CLUSTERS - the name of the file that contains the definitions of all 
                          the kernels for PAMM You can use multiple instances of this 
                          keyword i.e. CLUSTERS1, CLUSTERS2, CLUSTERS3... 
             REGULARISE - ( default=0.001 ) don't allow the denominator to be smaller 
                          then this value 

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 
                 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 
                    SUM - calculate the sum of all the quantities. The final value 
                          can be referenced using <em>label</em>.sum. You can use 
                          multiple instances of this keyword i.e. SUM1, SUM2, SUM3... The 
                          corresponding values are then referenced using <em>label</em>.sum-1, 
                          <em>label</em>.sum-2, <em>label</em>.sum-3... 


