g_kinetics_d (1) - Linux Man Pages
g_kinetics_d: derives information about kinetic processes from you trajectories
NAMEg_kinetics - derives information about kinetic processes from you trajectories
SYNOPSISg_kinetics -f temp.xvg -d data.xvg -d2 data2.xvg -o ft_all.xvg -o2 it_all.xvg -o3 ft_repl.xvg -ee err_est.xvg -g remd.log -m melt.xvg -[no]h -nice int -tu enum -[no]w -[no]xvgr -[no]time -b real -e real -bfit real -efit real -T real -n int -cut real -ucut real -euf real -efu real -ei real -maxiter int -[no]back -tol real -skip int -[no]split -[no]sum -[no]discrete -mult int
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.
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 temperatureare 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 foled 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.
In order to compile this program you need access to the GNU scientific library.
FILES-f temp.xvg Input
-nice int 19
-tu enum ps
-b real 0
-e real 0
-bfit real -1
-efit real -1
-T real 298.15
-n int 1
-cut real 0.2
-ucut real 0
-euf real 10
-efu real 30
-ei real 10
-maxiter int 100
-tol real 0.001
-skip int 0
-mult int 1
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