On 2010-09-24 23.31, Justin A. Lemkul wrote:
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.
That's correct, and the RMSD is quantized by setting the cut-off value.
-Justin
thanks a lot
Kevin
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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