[gmx-users] gmx distance error - invalid index with -f vs -s input file

[Travis Meyer]

Hello all,

I am using gmx distance to extract bond distances from a set of 200 coarse-grained polymer molecules (10 "atoms" each). I created an index file pointing to all of the bonds, and ran the command as

gmx distance -f cg_traj.gro -n bonds.ndx -oh bondhist.xvg

However, I was getting an error message upon choosing which index group to use.

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

Both the .gro and .ndx file contain the correct atom indices (1-2000). Interestingly enough, when I sent the same .gro file to gmx distance using the -s tag, I was able to correctly get the bond distance histogram (albeit I do not believe it includes all time points from the trajectory).

Does anyone have any insight onto why switching from an input trajectory (-f) to an input structure (-s) using the same .gro file would alleviate the error above, or what could be causing that error when sending a trajectory? I am new to GROMACS/Molecular Dynamics, so any help would be greatly appreciated.

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