[gmx-users] fit versus nofit

[Oliver Carrillo]

Thank you very much for your fast answer!

Oliver

2017-04-12 12:01 GMT+02:00 David van der Spoel <spoel at xray.bmc.uu.se>:

> On 12/04/17 10:28, Oliver Carrillo wrote:
>
>> Dear users,
>>
>> I wonder what is the difference between these two procedures:
>>
>> trjconv -s TYR.MD.tpr -f trajout.centered.xtc -FIT rot+trans -n
>>>
>> index_presolo2.ndx -o trajout.cent.fit.xtc
>>
>>> g_covar -f trajout.cent.fit.xtc -s TYR.MD.tpr -n index_presolo2.ndx -o
>>>
>> eigenvaltyr.xvg -v eigenvec2.trr -NOFIT
>>
>> and this one,
>>
>> g_covar -f trajout.centered.xtc -s TYR.MD.tpr -n index_presolo2.ndx -o
>>>
>> eigenvaltyr.xvg -v eigenvec2.trr -FIT
>>
>> always fitting with respect to the same group of atoms.
>>
>> I get different eigenvectors for each procedure but I think they should be
>> the same
>>
> The question is "how different". Numerically it can differ because you are
> storing the fitted trajectory in a limited precision trajectory file.
>
> You could try running gmx check -f -f2 on the output files.
>
>>
>> Thanks!
>> Oliver
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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