# When I run hbond, an error occurs in the step "Merging hbonds with Acceptor and Donor swapped." **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [June 24, 2024, 6:39am UTC](https://gromacs.bioexcel.eu/t/when-i-run-hbond-an-error-occurs-in-the-step-merging-hbonds-with-acceptor-and-donor-swapped/9488 "2024-06-24T06:39:27Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![D2390](https://avatars.discourse-cdn.com/v4/letter/d/8c91f0/32.png) [@D2390](https://gromacs.bioexcel.eu/u/D2390)\ **Post date:** [June 24, 2024, 6:39am UTC](https://gromacs.bioexcel.eu/t/when-i-run-hbond-an-error-occurs-in-the-step-merging-hbonds-with-acceptor-and-donor-swapped/9488/1 "2024-06-24T06:39:27Z")
GROMACS version:gromacs2023 GROMACS modification: Yes/No Here post your question The server is using 200g of RAM, there shouldn’t be an out of memory problem, I used the command submitted by sbatch： #!/bin/bash #SBATCH -J gromacs2023 #SBATCH -p amd #SBATCH -N 1 #SBATCH --ntasks-per-node=128 #SBATCH --mem=200G module purge #module load compiler/intel/2017.5.239 #module load mpi/intelmpi/2017.4.239 #module load mpi/hpcx/2.4.1/intel-2017.5.239 #module load apps/gromacs/2019.5/hpcx-2.4.1-intel2017 module load compiler/intel-compiler/2021.3.0 module load mpi/intelmpi/2021.3.0 module load apps/cmake/3.26.3 module load compiler/gcc/9.3.0 module load mathlib/fftw/intelmpi/3.3.9\_single module load apps/gromacs/2023/cpu-intelmpi-intel2021 echo -e “1\n13” | gmx\_mpi hbond -f md.xtc -s md.tpr -n index.ndx -num -hbm -hbn I successfully ran mdrun for 25ns, generating files: md.tpr, md.xtc. Here is the command I executed: Select a group: Selected 1: ‘Protein’ Select a group: Selected 13: ‘MOL’ Checking for overlap in atoms between Protein and MOL Calculating hydrogen bonds between Protein (11283 atoms) and MOL (65 atoms) Found 982 donors and 2019 acceptors Making hbmap structure…done. Reading frame 0 time 0.000 Will do grid-search on 25x25x25 grid, rcut=0.34999999 Frame loop parallelized with OpenMP using 128 threads. Reading frame 12000 time 24000.000 Found 52 different hydrogen bonds in trajectory Found 114 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 325/982[comput24:41390:0:41390] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil)) ==== backtrace (tid: 41390) ==== 0 0x0000000000014070 .annobin\_sigaction.c() sigaction.c:0 1 0x0000000000fffbc3 \_INTERNALb7fb3a0b::do\_merge() gmx\_hbond.cpp:0 2 0x0000000000fff4c9 \_INTERNALb7fb3a0b::merge\_hb() gmx\_hbond.cpp:0 3 0x0000000000ff7fc5 gmx\_hbond() ???:0 4 0x0000000000e17207 gmx::CommandLineModuleManager::run() ???:0 5 0x000000000040aa8a main() ???:0 6 0x0000000000027453 \_\_libc\_start\_main() ???:0 7 0x000000000040a929 \_start() ???:0 /opt/gridview/slurm/spool/slurmd/job15569/slurm\_script: line 20: 41389 Done echo -e “1\n13” 41390 Segmentation fault (core dumped) | gmx\_mpi hbond -f md.xtc -s md.tpr -n index.ndx -num -hbm -hbn ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [June 24, 2024, 12:57pm UTC](https://gromacs.bioexcel.eu/t/when-i-run-hbond-an-error-occurs-in-the-step-merging-hbonds-with-acceptor-and-donor-swapped/9488/2 "2024-06-24T12:57:14Z")
The `gmx hbond` tool was rewritten in GROMACS 2024 and the old version has been deprecated. So, I’m afraid there will almost certainly not be any bug fixes to the 2023 version. However, there are still some features that have not yet been implemented. It would be good to hear if the 2024 version works, and/or what features you are missing from it.