[gmx-users] data.xvg for g_kinetics ?

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 24 23:31:44 CEST 2010

feng chen wrote:
> Hi gromacs user,
>    We recently ran in this problem when try to analyise our REMD 
> trajectories. g_kinetics module will be used for such kinda analysis, 
> however it looks like we need provide 2 xvgs file as input. The temp.xvg 
> we can get from demux.pl <http://demux.pl> and the other one (data.xvg) 
> we are not sure how to get . To get a better understanding of this  
> g_kinetics module, we have read through that reference paper, but 
> throught the that whole paper (Phys. Rev. Lett. 96, 
> <http://dx.doi.org/10.1103/PhysRevLett.96.238102>) there's no hint about 
> how to prepare this data.xvg file.
>    So, we were wondering , can anybody kindly let us know how did u guys 
> get this data.xvg file?

The content of the second input file is dependent upon how you assess folding. 
The paper you reference, IIRC, used RMSD as this indicator.  In principle, you 
should be able to use other metrics like R(g), native contacts, etc.


>    thanks a lot
>    Kevin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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