# Range checking error (gmx covar) **URL:** \ **Category:** User discussions\ **Created:** [February 4, 2021, 1:23pm UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542 "2021-02-04T13:23:43Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![purvi.gupta](https://avatars.discourse-cdn.com/v4/letter/p/6a8cbe/32.png) [@purvi.gupta](https://gromacs.bioexcel.eu/u/purvi.gupta)\ **Post date:** [February 4, 2021, 1:23pm UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542/1 "2021-02-04T13:23:43Z")
GROMACS version: 2020.5 Dear, I am trying to calculate the covariance for my system using gmx covar and C-alpha for the least squares fit. However, it gives me the following error: “Range checking error (possible bug): The provided structure file only contains 55028 coordinates, but coordinate index 3771 was requested for fitting. Make sure to update structure files and index files if you store only a part of the system” While applying PBC, I save the whole system in the trajectory. Therefore, I do not understand why this error shows up. Regards Purvi ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [February 5, 2021, 2:58pm UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542/2 "2021-02-05T14:58:48Z")
Hi I can not understand what can be the problem. Can you provide more information on the command line, you used? Thank you Alessandra ---
**Author:** ![purvi.gupta](https://avatars.discourse-cdn.com/v4/letter/p/6a8cbe/32.png) [@purvi.gupta](https://gromacs.bioexcel.eu/u/purvi.gupta)\ **Post date:** [February 8, 2021, 9:36am UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542/3 "2021-02-08T09:36:42Z")
Hi Alessandra, Thank you for the reply. I use the command “gmx covar -s md.tpr -f md.xtc” for calculating the covariance matrix. The system consists of a protein in a cubic box with tip3p water model. It works if I run the same command on supercomputer where the production MD was performed but not on my personal system. Kindest Regards Purvi Gupta ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [February 8, 2021, 10:14am UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542/4 "2021-02-08T10:14:01Z")
This is a bug in src/gromacs/gmxana/gmx\_covar.cpp. Line 92 is: if (largestIndex \< largestOkayIndex) But should be: if (largestIndex \>= largestOkayIndex) If you installed Gromacs yourself, you can change this yourself, recompile and install. ---
**Author:** ![purvi.gupta](https://avatars.discourse-cdn.com/v4/letter/p/6a8cbe/32.png) [@purvi.gupta](https://gromacs.bioexcel.eu/u/purvi.gupta)\ **Post date:** [February 8, 2021, 1:57pm UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542/5 "2021-02-08T13:57:34Z")
Dear Hess, Thank you so much. It works now. :) Kindest Regards Purvi Gupta ---
**Author:** ![Santhosh\_Tomm](https://avatars.discourse-cdn.com/v4/letter/s/c5a1d2/32.png) [@Santhosh\_Tomm](https://gromacs.bioexcel.eu/u/Santhosh_Tomm)\ **Post date:** [September 23, 2025, 7:44am UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542/6 "2025-09-23T07:44:28Z")
Hi, Recently in the GROMACS 2025.2 version, during COVAR analysis, i encountered the same error, which is as follows: My command line: gmx covar -s protein\_whole.gro -f trajector\_conv\_forlig\_final\_whole.xtc -b 110 -e 490 -tu ns -o eigenvalues\_NAP\_whole.xvg -av average\_structure\_NAP\_whole.pdb -v eigenvectors\_NAP\_whole.trr -xpma covapic\_NAP\_whole.xpm -n index\_classification.ndx Program: gmx covar, version 2025.2 Source file: src/gromacs/gmxana/gmx\_covar.cpp (line 108) Function: void gmx::{anonymous}::throwErrorIfIndexOutOfBounds(gmx::ArrayRef, int, const std::string&) Range checking error (possible bug): The provided structure file only contains 30872 coordinates, but coordinate index 31684 was requested for fitting. Make sure to update the structure files and index files if you store only a part of your system. My trajectory and structure are created out of the same index group. Please let me know, how to fix this. ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [September 25, 2025, 7:09am UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542/7 "2025-09-25T07:09:16Z")
If you reduced you trajectory and structure file using an index group, you should create a new index file for that new structure file. ---
**Author:** ![Santhosh\_Tomm](https://avatars.discourse-cdn.com/v4/letter/s/c5a1d2/32.png) [@Santhosh\_Tomm](https://gromacs.bioexcel.eu/u/Santhosh_Tomm)\ **Post date:** [September 25, 2025, 9:34am UTC](https://gromacs.bioexcel.eu/t/range-checking-error-gmx-covar/1542/8 "2025-09-25T09:34:35Z")
Thanks for the reply. I will try it out.