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       g_kinetics - estimate rate constants


       g_kinetics  -f  temp.xvg  -d  data.xvg  -o  ft_all.xvg  -g  remd.log -m
       melt.xvg [other options...]


       g_kinetics reads  two  xvg  files,  each  one  containing  data  for  N
       replicas.   The  first file contains the temperature of each replica at
       each  timestep  and  the  second  contains  real  values  that  can  be
       interpreted  as  an  indicator for folding. If the value in the file is
       larger than the cutoff it is taken to be unfolded  and  the  other  way
       around.[PAR]  From  these  data an estimate of the forward and backward
       rate constants for folding is  made  at  a  reference  temperature.  In
       addition,  a theoretical melting curve and free energy as a function of
       temperature are printed in an xvg file.

       The user can give a max value to be regarded as  intermediate  (-ucut),
       which,  when given will trigger the use of an intermediate state in the
       algorithm to be defined as those structures that have cutoff <  DATA  <
       ucut. Structures with DATA values larger than ucut will not be regarded
       as potential folders. In this case 8 parameters are optimized.

       The average fraction folded is printed in an xvg file together with the
       fit  to  it.   If  an intermediate is used a further file will show the
       build of the intermediate and the fit to that process.

       The program can also be used  with  continuous  variables  (by  setting
       -nodiscrete).  In this case kinetics of other processes can be studied.
       This is very much a  work  in  progress  and  hence  the  manual  (this
       information) is lagging behind somewhat.


        Option     Filename  Type         Description
         -f       temp.xvg  Input        xvgr/xmgr file
         -d       data.xvg  Input        xvgr/xmgr file
        -d2      data2.xvg  Input, Opt.  xvgr/xmgr file
         -o     ft_all.xvg  Output       xvgr/xmgr file
        -o2     it_all.xvg  Output, Opt. xvgr/xmgr file
        -o3    ft_repl.xvg  Output, Opt. xvgr/xmgr file
        -ee    err_est.xvg  Output, Opt. xvgr/xmgr file
         -g       remd.log  Output       Log file
         -m       melt.xvg  Output       xvgr/xmgr file


       Option       Type   Value   Description
       -[no]h       bool   no      Print help info and quit
       -[no]X       bool   no      Use dialog box GUI to edit command line options
       -nice        int    19      Set the nicelevel
       -tu          enum   ps      Time unit: ps, fs, ns, us, ms or s
       -[no]w       bool   no      View output xvg, xpm, eps and pdb files
       -[no]xvgr    bool   yes     Add specific codes (legends etc.) in the output
                                   xvg files for the xmgrace program
       -[no]time    bool   yes     Expect a time in the input
       -b           real   0       First time to read from set
       -e           real   0       Last time to read from set
       -bfit        real   -1      Time to start the fit from
       -efit        real   -1      Time to end the fit
       -T           real   298.15  Reference temperature for computing rate constants
       -n           int    1       Read data for # replicas. Only necessary when
                                   files are written in xmgrace format using @type
                                   and & as delimiters.
       -cut         real   0.2     Cut-off (max) value for regarding a structure as
       -ucut        real   0       Cut-off (max) value for regarding a structure as
                                   intermediate (if not folded)
       -euf         real   10      Initial guess for energy of activation for
                                   folding (kJ/mole)
       -efu         real   30      Initial guess for energy of activation for
                                   unfolding (kJ/mole)
       -ei          real   10      Initial guess for energy of activation for
                                   intermediates (kJ/mole)
       -maxiter     int    100     Max number of iterations
       -[no]back    bool   yes     Take the back reaction into account
       -tol         real   0.001   Absolute tolerance for convergence of the Nelder
                                   and Mead simplex algorithm
       -skip        int    0       Skip points in the output xvg file
       -[no]split   bool   yes     Estimate error by splitting the number of
                                   replicas in two and refitting
       -[no]sum     bool   yes     Average folding before computing chi^2
       -[no]discrete  bool yes     Use a discrete folding criterium (F <-> U) or a
                                   continuous one
       -mult        int    1       Factor to multiply the data with before



       More   information   about   the   GROMACS   suite   is   available  in
       /usr/share/doc/gromacs or at

       Implementation details have been published  in  Phys.  Rev.  Lett.  96,
       238102 (2006), <>.