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

[Travis Meyer]

    Thanks for your response! I checked and the cg_traj file contains atoms numbered 1-2000, which matches the atom IDs from the index file. The same trajectory does work using gmx angle with an angle index file created from the same python script which also includes atom IDs 1-2000 as well.
    The fact that the error says "largest allowed atom index is 0" seems especially interesting to me, as it implies the gmx distance isn't finding any atoms in the trajectory file.
    Travis Meyer, Ph.D.
    INSPIRE Postdoctoral Fellow
    Gormley Lab, Rutgers University
    > 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 (
    > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcgmartini.nl%2Findex.php%2Ftutorials-general-introduction-gmx5%2Fmartini-tutorials-polymers-gmx5&data=02%7C01%7Ctravis.meyer%40rutgers.edu%7Cf110fee0c56e442a988308d79b7a1aee%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C637148821067442954&sdata=rBs2IvNHERRNN5IQbflOJCGJezD4jVHWREeFC2%2FMTuY%3D&reserved=0)
    > 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:
    >

- Ignored:
    > I am not familiar with the MARTINI tutorial, but I guess that the
    particles numbers in your traj_cg are different from the one of
    traj_allatoms.
    Thus my suggestion is to check that the numbers reported in the index file
    corresponds to the particles number that you have in your traj_cg.
    The easy way to do it is to look  at  CG_gro file ( you can generate using
    gmx traj in the same way that you have used for traj_cg

    Best regards
    Alessandra



    > 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!

Travis Meyer, Ph.D.
INSPIRE Postdoctoral Fellow
Gormley Lab, Rutgers University