g_kinetics_d

Langue: en

Version: 259090 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

NAME

g_kinetics - estimate rate constants

SYNOPSIS

g_kinetics -[no]h [other options...]

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.[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.

OPTIONS

-[no]h
Print help info and quit (default: no).

Other options are available but not currently well documented.

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at http://www.gromacs.org/.

Implementation details have been published in Phys. Rev. Lett. 96, 238102 (2006), <http://dx.doi.org/10.1103/PhysRevLett.96.238102>.