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

                  ATOMS - the 4 atoms involved in each of the bonds for which you 
                          wish to calculate the J-coupling. Keywords like ATOMS1, ATOMS2, 
                          ATOMS3,... should be listed and one J-coupling will be calculated for 
                          each ATOMS keyword you specify. You can use multiple instances 
                          of this keyword i.e. ATOMS1, ATOMS2, ATOMS3... 

The following arguments are compulsory: 

              NOISETYPE - ( default=MGAUSS ) functional form of the noise 
                          (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC) 
             LIKELIHOOD - ( default=GAUSS ) the likelihood for the GENERIC 
                          metainference model, GAUSS or LOGN 
                DFTILDE - ( default=0.1 ) fraction of sigma_mean used to evolve 
                          ftilde 
                 SCALE0 - ( default=1.0 ) initial value of the scaling factor 
            SCALE_PRIOR - ( default=FLAT ) either FLAT or GAUSSIAN 
                OFFSET0 - ( default=0.0 ) initial value of the offset 
           OFFSET_PRIOR - ( default=FLAT ) either FLAT or GAUSSIAN 
                 SIGMA0 - ( default=1.0 ) initial value of the uncertainty parameter 
              SIGMA_MIN - ( default=0.0 ) minimum value of the uncertainty parameter 
              SIGMA_MAX - ( default=10. ) maximum value of the uncertainty parameter 
           OPTSIGMAMEAN - ( default=NONE ) Set to NONE/SEM to manually set sigma 
                          mean, or to estimate it on the fly 
           WRITE_STRIDE - ( default=10000 ) write the status to a file every N steps, 
                          this can be used for restart/continuation 
                   TYPE - Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM) 

In addition you may use the following options: 

  NUMERICAL_DERIVATIVES - ( default=off ) calculate the derivatives for these 
                          quantities numerically 
                DOSCORE - ( default=off ) activate metainference 
             NOENSEMBLE - ( default=off ) don't perform any replica-averaging 
               REWEIGHT - ( default=off ) simple REWEIGHT using the ARG as energy 
              SCALEDATA - ( default=off ) Set to TRUE if you want to sample a scaling 
                          factor common to all values and replicas 
              ADDOFFSET - ( default=off ) Set to TRUE if you want to sample an offset 
                          common to all values and replicas 
                  NOPBC - ( default=off ) ignore the periodic boundary conditions 
                          when calculating distances 
                    ARG - the input for this action is the scalar output from one or 
                          more other actions. The particular scalars that you will use are 
                          referenced using the label of the action. If the label appears on its 
                          own then it is assumed that the Action calculates a single 
                          scalar value. The value of this scalar is thus used as the input 
                          to this new action. If * or *.* appears the scalars calculated 
                          by all the proceeding actions in the input file are taken. 
                          Some actions have multi-component outputs and each component of 
                          the output has a specific label. For example a \ref DISTANCE 
                          action labelled dist may have three components x, y and z. To take 
                          just the x component you should use dist.x, if you wish to take 
                          all three components then use dist.*.More information on the 
                          referencing of Actions can be found in the section of the manual on the 
                          PLUMED \ref Syntax. Scalar values can also be referenced using 
                          POSIX regular expressions as detailed in the section on \ref 
                          Regex. To use this feature you you must compile PLUMED with the 
                          appropriate flag. You can use multiple instances of this keyword i.e. 
                          ARG1, ARG2, ARG3... 
              AVERAGING - Stride for calculation of averaged weights and sigma_mean 
              SCALE_MIN - minimum value of the scaling factor 
              SCALE_MAX - maximum value of the scaling factor 
                 DSCALE - maximum MC move of the scaling factor 
             OFFSET_MIN - minimum value of the offset 
             OFFSET_MAX - maximum value of the offset 
                DOFFSET - maximum MC move of the offset 
            REGRES_ZERO - stride for regression with zero offset 
                 DSIGMA - maximum MC move of the uncertainty parameter 
            SIGMA_MEAN0 - starting value for the uncertainty in the mean estimate 
        SIGMA_MAX_STEPS - Number of steps used to optimise SIGMA_MAX, before that the 
                          SIGMA_MAX value is used 
                   TEMP - the system temperature - this is only needed if code 
                          doesn't pass the temperature to plumed 
               MC_STEPS - number of MC steps 
           MC_CHUNKSIZE - MC chunksize 
            STATUS_FILE - write a file with all the data useful for 
                          restart/continuation of Metainference 
               SELECTOR - name of selector 
                NSELECT - range of values for selector [0, N-1] 
                RESTART - allows per-action setting of restart (YES/NO/AUTO) 
                      A - Karplus parameter A 
                      B - Karplus parameter B 
                      C - Karplus parameter C 
                  SHIFT - Angle shift in radians 
               COUPLING - Add an experimental value for each coupling You can use 
                          multiple instances of this keyword i.e. COUPLING1, COUPLING2, 
                          COUPLING3... 


