[gmx-users] data.xvg for g_kinetics ?
David van der Spoel
spoel at xray.bmc.uu.se
Sat Sep 25 09:33:43 CEST 2010
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.
>> thanks a lot
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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