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

                  ATOMS - 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. For more information on 
                          how to specify lists of atoms see \ref Group 
              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. A list of hydrogen 
                          atoms is always required even if you specify the other atoms 
                          using DONORS and ACCEPTORS as described below.. For more 
                          information on how to specify lists of atoms see \ref Group 
                 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 

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 - The \ref switchingfunction that specifies how close a pair 
                          of atoms must be together for there to be a hydrogen bond 
                          between them You can use multiple instances of this keyword i.e. 
                          SWITCH1, SWITCH2, SWITCH3... 
                HSWITCH - The \ref switchingfunction that specifies how close the 
                          hydrogen must be to the donor atom of the hydrogen bond for it to be 
                          considered a hydrogen bond You can use multiple instances of this 
                          keyword i.e. HSWITCH1, HSWITCH2, HSWITCH3... 
                ASWITCH - A \ref switchingfunction that is used to specify what the 
                          angle between the vector connecting the donor atom to the 
                          acceptor atom and the vector connecting the donor atom to the 
                          hydrogen must be in order for it considered to be a hydrogen bond 
                          You can use multiple instances of this keyword i.e. ASWITCH1, 
                          ASWITCH2, ASWITCH3... 
                    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... 


