Segmentation Fault using covar?

User discussions
1

GROMACS version: 2023
GROMACS modification: No

Some context as to why I’m somewhat confused right now :

I was able to perform gmx covar on my device and generate a set of eigenvalues and eigenvectors.

My issue comes later when I perform anaeig. I’m using a certain tutorial, and for some reason, the following scripts are giving me segmentation errors (11 on mac, core dumped on linux)

Tutorial I’m following:
http://www3.mpibpc.mpg.de/groups/de_groot/compbio/p4/index.html

Anaeig script:
gmx anaeig -s ref.pdb -f md1_backbone.xtc -proj -first 1 -last 6

I guess I’m just confused and frustrated as to how my system is able to do the PCA calculations yet anaeig is messing with me. Any feedback would be much appreciated, thanks.

2

Hi!

This is a bug in GROMACS 2023. You can use GROMACS 2022.5 instead or use the workaround described here: Gromacs 2023: Segmentation fault with gmx anaeig (but no problem with Gromacs 2022.4) - #4 by al42and.

The bug will be fixed in GROMACS 2023.1, to be released by the end of April.

3

Hi! Apologies for the quite late response. I just did want to say Thank You! I’ll be adjusting with the work around.