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.
-Justin
thanks a lot
Kevin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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