# Segmentation fault (core dumped) with ndx file

**URL:** <https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped-with-ndx-file/4279>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [June 8, 2022, 7:53am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped-with-ndx-file/4279 "2022-06-08T07:53:01Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ag94](https://avatars.discourse-cdn.com/v4/letter/a/ecc23a/32.png) [@ag94](https://gromacs.bioexcel.eu/u/ag94)\
**Post date:** [June 8, 2022, 7:53am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped-with-ndx-file/4279/1 "2022-06-08T07:53:01Z")

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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.

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [June 14, 2022, 10:29am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped-with-ndx-file/4279/2 "2022-06-14T10:29:36Z")

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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

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**Author:** ![ebriand](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ebriand/32/2314_2.png) [@ebriand](https://gromacs.bioexcel.eu/u/ebriand)\
**Post date:** [June 16, 2022, 9:17am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped-with-ndx-file/4279/3 "2022-06-16T09:17:11Z")

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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.