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

[Alessandra Villa]

Hi,

On Tue, Jan 14, 2020 at 7:41 PM Travis Meyer <travis.meyer at rutgers.edu>
wrote:

> 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:
>
> 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!
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