Segmentation fault (core dumped) with ndx file

User discussions
1

GROMACS version:2020.5
GROMACS modification: Yes/No

Hi, I am a beginner in MD simulation. I have run a 550 ns simulation of a membrane protein. Then I made an index file to calculate parameters of select portion of the protein. When I tried to run rms function to get rmsd-vs-average.xvg (-f step7noPBC.xtc -s average.pdb -n res.ndx), I am able to select the group containing the selected region but in the next step I get this error-Segmentation fault (core dumped).
I was able to use the same index file for getting
rmsf( -s step7.tpr -f step7noPBC.xtc -n res.ndx -o rmsf-per-residue.xvg -ox average.pdb)
and rmsd(-s step7.tpr -f step7noPBC.xtc -o rmsd.xvg -tu ns -n res.ndx),
but somehow in the said step it is not working out. Please help me solve this.

2

Hi,

when you run
gmx rms -f step7noPBC.xtc -s average.pdb -n res.ndx
source of error could be xtc file and the average.pdb do not contains the same system, or the index file is generated of a different system. For example a problem could be that average.pdb is contain only a part of the system and the index file is genetated from the whole system.

Regards
Alessandra

3

While the error is likely to be a file content mistake as described in the previous message, generally user input error should not cause segmentation fault, rather output an error message - so, to fix this in future release of gromacs, it would be useful if you could post the input files (.pdb, .xtc, .ndx, .tpr) necessary to reproduce this.