[gmx-users] clarification regarding input format for g_kinetics

[David van der Spoel]

On 15/07/15 18:24, Smith, Micholas D. wrote:
> Just tried it. Seems to work.
>
> To be clear, the data.xvg file should created from the demuxed trajectories, right?
>
Yes.

> Thanks for the help. Sorry for a kind of silly question.
Not silly at all, not many people use this I'm afraid. Please check your 
results anyway.

>
> ===================
> 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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-- 
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