Hello all,

I am a brand new GROMACS/MD User, and I've run into an error message during analysis that I can't figure out. I am interested in CG modeling using the MARTINI field, and have been following a tutorial on that site for parametrizing CG bonded interactions from an all-atom simulation ( http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/martini-tutorials-polymers-gmx5).

Following the tutorial, I have successfully created CG psuedo-atoms from the all-atom trajectory, and the error I am running into comes from trying to extract the bonded parameters from this trajectory. I created index files for all of the bonds, angles, and dihedrals I need to analyze, and am trying to analyze these values. I can use the "gmx angle" command to get distributions of bond angles and dihedrals successfully using the CG trajectory and appropriate index files. However, I get an error when using the "gmx bond" command to get bond lengths.

" 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). "

I've gone in and checked both the trajectory and index files, and they both contain the correct atom IDs (1-2000). The fact that it says the largest allowed atom index is 0 to me implies the error lies with the trajectory rather than the index files, and yet the exact same trajectory works fine with "gmx angle".

Any recommendations for next troubleshooting steps would be much appreciated.

Thanks!

Travis