[gmx-users] Troubleshooting Error Message: Invalid Index Group References

[Travis Meyer]

Hello all,

I am a brand new MD/GROMACS user, and I have been trying to learn how to use GROMACS for coarse-grained simulations using the MARTINI forcefield. I was going through a tutorial on coarse-graining from the MARTINI website (http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/martini-tutorials-polymers-gmx5) but ran into an error I have been not been able to find a solution for.

After coarse-graining the all-atom simulation to the COM between 3 atoms, I need to calculate bond lengths and angles in order to parameterize bonded interactions. Following instructions from the tutorial, I created index files for all bonds, angles, and dihedrals and used gmx distance along with the coarse-grained trajectory file. After choosing which index group I want to use, I receive an error message:

Inconsistency in user input: Invalid index group references encountered
Group 'bonds_core1' cannot be used in selections, because it contains negative atom indices and/or references atoms not present (largest allowed atom index is 0).

The index file itself contains all the proper atom indices. The fact that the error says "largest allowed atom index is 0" makes me think there is an error with my .xtc file, but I did not receive any errors when calculating angle distributions using the exact same trajectory file and appropriate angle index files.

Are there any recommendations for how to go about fixing this?

Thanks!