g_kinetics (1) - Linux Man Pages

g_kinetics: derives information about kinetic processes from you trajectories

NAME

g_kinetics - derives information about kinetic processes from you trajectories

VERSION 4.0.1

SYNOPSIS

g_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

DESCRIPTION

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.

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
 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 

OTHER OPTIONS

-[no]hno
 Print help info and quit

-nice int 19
 Set the nicelevel

-tu enum ps
 Time unit:  ps fs ns us ms or  s

-[no]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[no]timeyes
 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]backyes
 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]splityes
 Estimate error by splitting the number of replicas in two and refitting

-[no]sumyes
 Average folding before computing chi2

-[no]discreteyes
 Use a discrete folding criterium (F - U) or a continuous one

-mult int 1
 Factor to multiply the data with before discretization

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.