[gmx-users] clarification regarding input format for g_kinetics

Smith, Micholas D. smithmd at ornl.gov
Wed Jul 15 14:20:10 CEST 2015

I was looking to use g_kinetics, and was slightly confused by the input options, and was hoping someone could help clarify.

An example case of using g_kinetics is:

g_kinetics -f temp.xvg -d data.xvg -o ft_all.xvg -o2 it_all.xvg -o3 ft_repl.xvg -m melt.xvg -ee err_est.xvg

>From what I can ascertain, temp.xvg is generated from using the demux.pl script (the output file remd_temps.xvg?); and I know data.xvg should be a flat file that has an "indicator of folding/unfolding" in it; however, what I am confused about is should data.xvg be a multi-column file with the first column being "time" followed by one column per demuxed replica trajectory of the current state of the "indicator," i.e 1 if "folded" and 0 "unfolded". Something that looks like this

0  1 1 1 ....0 0 0 0

1  1 0 0 ....1 0 0 1


and so on.

Thanks in advanced for the help.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

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