Range checking error (gmx covar)

User discussions
1

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

2

Hi
I can not understand what can be the problem. Can you provide more information on the command line, you used?
Thank you
Alessandra

3

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

4

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.

5

Dear Hess,

Thank you so much. It works now. :)

Kindest Regards
Purvi Gupta

6

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.

7

If you reduced you trajectory and structure file using an index group, you should create a new index file for that new structure file.

8

Thanks for the reply. I will try it out.