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

                  ATOMS - the atoms involved in each of the contacts you wish to 
                          calculate. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed 
                          and one contact will be calculated for each ATOM keyword you 
                          specify.. You can use multiple instances of this keyword i.e. ATOMS1, 
                          ATOMS2, ATOMS3... 

The following arguments are compulsory: 

                 SWITCH - The switching functions to use for each of the contacts in 
                          your map. You can either specify a global switching function 
                          using SWITCH or one switching function for each contact. Details 
                          of the various switching functions you can use are provided on 
                          \ref switchingfunction.. You can use multiple instances of this 
                          keyword i.e. SWITCH1, SWITCH2, SWITCH3... 

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 
                    SUM - ( default=off ) calculate the sum of all the contacts in 
                          the input 
                 CMDIST - ( default=off ) calculate the distance with respect to the 
                          provided reference contact map 
                 SERIAL - ( default=off ) Perform the calculation in serial - for 
                          debug purpose 
              REFERENCE - A reference value for a given contact, by default is 0.0 
                          You can either specify a global reference value using REFERENCE 
                          or one reference value for each contact.. You can use multiple 
                          instances of this keyword i.e. REFERENCE1, REFERENCE2, REFERENCE3... 
                 WEIGHT - A weight value for a given contact, by default is 1.0 You 
                          can either specify a global weight value using WEIGHT or one 
                          weight value for each contact.. You can use multiple instances of 
                          this keyword i.e. WEIGHT1, WEIGHT2, WEIGHT3... 


