Gmx mindist freezes while reading input

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1

GROMACS version: 2021.5
GROMACS modification: No

I am using gmx mindist to measure coarse grained structures with the solvent removed. I am also measuring the same trajectories with the structures reduced to either main- or side-chain representation. All of these measurements I am making at a few different concentrations. Here is what my usual invocation looks like:
gmx mindist -f vmd/2cg128_0ns-end.gro -s cg128/cg128-10/table.tpr -n cg128/cg128-10/index.ndx -on agg/contacts_2cg128_0ns-end_rc1.2.xvg -d 1.2

The execution freezes while reading some input structure files, i.e. the output prints "Reading frame 0 time 0.000" but never advances.

Changing the cutoff radius between 0.6 and 1.2 does not seem to fix this problem for a given file. The problem also does not seem related to particle counts or file size. On that note all trajectories are less than 1GB, and I think should easily fit in memory. My .gro files appear correct even for problem structures.

Any advice on this? I wonder if there’s a tpr issue I’m missing, but again for some files the calculations complete without any trouble.

Thanks for reading!

2

Hi,
did you get any other error? Did the machine freeze or just the command line?
If you think there may be an error in the tpr file you can check the status of your tpr using gmx dump. A alternative is to use a gro file in place of the tpr file.
I hope it helps
\Alessandra