g_kinetics(1) 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