[gmx-users] clarification regarding input format for g_kinetics
Smith, Micholas D.
smithmd at ornl.gov
Wed Jul 15 18:24:17 CEST 2015
Just tried it. Seems to work.
To be clear, the data.xvg file should created from the demuxed trajectories, right?
Thanks for the help. Sorry for a kind of silly question.
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
Sent: Wednesday, July 15, 2015 12:13 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] clarification regarding input format for g_kinetics
On 15/07/15 14:20, Smith, Micholas D. wrote:
> 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
That looks OK. Have you tried it?
> 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
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 hxxp://folding.bmc.uu.se
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