[gmx-users] fit versus nofit

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 12 12:01:55 CEST 2017

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.

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