SYNOPSISg_kinetics -f temp.xvg -d data.xvg -o ft_all.xvg -g remd.log -m melt.xvg [other options...]
DESCRIPTIONg_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 folded -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 discretization