Segmentation fault during gmx hbond

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1

GROMACS version:2020.2
GROMACS modification: No
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Command: gmx hbond -f trajout.xtc -s em16.tpr -num hbnum.xvg -hbm hbmap.xpm -hbn hbond.ndx -nomerge

Reading file em16.tpr, VERSION 2018.4 (single precision)
Note: file tpx version 112, software tpx version 119
Specify 2 groups to analyze:
Selected 1: ‘Protein’
Selected 1: ‘Protein’
Calculating hydrogen bonds in Protein (177 atoms)
Found 18 donors and 34 acceptors
Making hbmap structure…done.
Reading frame 0 time 2.000
Will do grid-search on 23x23x23 grid, rcut=0.34999999
Frame loop parallelized with OpenMP using 6 threads.
Reading frame 20 time 22.000
Found 53 different hydrogen bonds in trajectory
Found 98 different atom-pairs within hydrogen bonding distance
Average number of hbonds per timeframe 7.267 out of 306 possible
Segmentation fault (core dumped)

Due to this error, no matrix file was created. What could be wrong here?

2

Hi,

You’re using a mismatched gromacs version from what was used to create the tpr, and an older gromacs version. Can you install Gromacs 2020.3, recreate the tpr, and redo the analysis?