Provided by: gromacs-data_4.6.5-1build1_all bug


       g_kinetics - estimate rate constants


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


       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),  <‐>.