# \#gmx-hbond **URL:** https://gromacs.bioexcel.eu/tag/gmx-hbond/62.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## ["Segmentation fault", "std::bad\_alloc" and "malloc(): invalid size" when running gmx hbond](https://gromacs.bioexcel.eu/t/segmentation-fault-std-bad-alloc-and-malloc-invalid-size-when-running-gmx-hbond/6566)
**Author:** [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\ **Replies:** 11\ **Last updated:** [April 30, 2026, 8:05pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-std-bad-alloc-and-malloc-invalid-size-when-running-gmx-hbond/6566 "2026-04-30T20:05:19Z")
GROMACS version: 2023 GROMACS modification: Yes, but hbond has not been touched Hi, I keep getting ‘low level’ errors when running gmx hbond -life with Gromacs 2023. When supplying a trajectory generated with a older … --- ## [How to compute the number of hydrogen bonds per molecule in a pure water system: gmx hbond](https://gromacs.bioexcel.eu/t/how-to-compute-the-number-of-hydrogen-bonds-per-molecule-in-a-pure-water-system-gmx-hbond/8244)
**Author:** [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)\ **Replies:** 1\ **Last updated:** [December 3, 2025, 1:47pm UTC](https://gromacs.bioexcel.eu/t/how-to-compute-the-number-of-hydrogen-bonds-per-molecule-in-a-pure-water-system-gmx-hbond/8244 "2025-12-03T13:47:08Z")
GROMACS version: 2022 GROMACS modification: No Hi, I’m trying to compute the number of hydrogen bonds per water molecule in a pure water system as my control for another simulation. But every time I run gmx hbond with… --- ## [Should I swap group order and sum results for hydrogen bond counts when using \`gmx hbond\`?](https://gromacs.bioexcel.eu/t/should-i-swap-group-order-and-sum-results-for-hydrogen-bond-counts-when-using-gmx-hbond/12733)
**Author:** [@liuwq](https://gromacs.bioexcel.eu/u/liuwq)\ **Replies:** 0\ **Last updated:** [October 5, 2025, 3:08am UTC](https://gromacs.bioexcel.eu/t/should-i-swap-group-order-and-sum-results-for-hydrogen-bond-counts-when-using-gmx-hbond/12733 "2025-10-05T03:08:45Z")
Hello everyone, Could you please guide me on whether it’s necessary to run gmx hbond twice? That said, for two different groups without overlapping, first input Group1 and then input Group2 in the prompt window. And the… --- ## [Help: Error encountered in gmx hbond hydrogen bond calculation](https://gromacs.bioexcel.eu/t/help-error-encountered-in-gmx-hbond-hydrogen-bond-calculation/12192)
**Author:** [@Yolo-kk](https://gromacs.bioexcel.eu/u/Yolo-kk)\ **Replies:** 2\ **Last updated:** [June 4, 2025, 7:34am UTC](https://gromacs.bioexcel.eu/t/help-error-encountered-in-gmx-hbond-hydrogen-bond-calculation/12192 "2025-06-04T07:34:31Z")
GROMACS version:2023.3 GROMACS modification: Yes/No Hello everyone, I currently want to use the gmx hbond command to calculate hydrogen bonds between specified protein atom groups. First, I generated the specified atom… --- ## [Strange numbers on hbnum.xvg - Hbond Analysis](https://gromacs.bioexcel.eu/t/strange-numbers-on-hbnum-xvg-hbond-analysis/11827)
**Author:** [@Daphney](https://gromacs.bioexcel.eu/u/Daphney)\ **Replies:** 1\ **Last updated:** [March 28, 2025, 2:18pm UTC](https://gromacs.bioexcel.eu/t/strange-numbers-on-hbnum-xvg-hbond-analysis/11827 "2025-03-28T14:18:43Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I used this command gmx hbond -f md\_0\_1.xtc -s md\_0\_1.tpr -n index.ndx -num hbnum.xvg for my analysis after creating an index file. However, I am g… --- ## [GMX hbond generating weird result](https://gromacs.bioexcel.eu/t/gmx-hbond-generating-weird-result/10951)
**Author:** [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Replies:** 4\ **Last updated:** [January 7, 2025, 5:47pm UTC](https://gromacs.bioexcel.eu/t/gmx-hbond-generating-weird-result/10951 "2025-01-07T17:47:07Z")
GROMACS version: GROMACS modification: Yes/No I have run 100ns protein-ligand simulation. However, the gmx hbond function gave a very weird result, command: gmx hbond -f md\_0\_100\_center.xtc -s md\_0\_100.tpr -tu ns -g h… --- ## [Hbond per residue is greater than the theoretical value](https://gromacs.bioexcel.eu/t/hbond-per-residue-is-greater-than-the-theoretical-value/10675)
**Author:** [@WangshuLi](https://gromacs.bioexcel.eu/u/WangshuLi)\ **Replies:** 0\ **Last updated:** [December 2, 2024, 2:03am UTC](https://gromacs.bioexcel.eu/t/hbond-per-residue-is-greater-than-the-theoretical-value/10675 "2024-12-02T02:03:12Z")
GROMACS version:2021.6 GROMACS modification: No i’ m using echo -e "8\\n16\\n" | gmx hbond -f rest\_3pc\_MD${i}\_topolmdtest\_50dt.xtc -s topolmdtest.tpr -num 50ns\_off\_rest\_3pc\_MD${i}\_topolmdtest\_50dt\_gmx\_hbond\_sc\_wat\_num.x… --- ## [Hbond issue with molecule](https://gromacs.bioexcel.eu/t/hbond-issue-with-molecule/10445)
**Author:** [@Sakho](https://gromacs.bioexcel.eu/u/Sakho)\ **Replies:** 1\ **Last updated:** [October 30, 2024, 7:12am UTC](https://gromacs.bioexcel.eu/t/hbond-issue-with-molecule/10445 "2024-10-30T07:12:15Z")
Hello GROMACS community, I’ve recently encountered an issue regarding hydrogen bonding analysis between a ligand and protein in my simulation. Initially. After running a short simulation (around 1 ns), I’m now facing a… --- ## [Gromacs Hbdons](https://gromacs.bioexcel.eu/t/gromacs-hbdons/10186)
**Author:** [@Sakho](https://gromacs.bioexcel.eu/u/Sakho)\ **Replies:** 0\ **Last updated:** [September 18, 2024, 9:46am UTC](https://gromacs.bioexcel.eu/t/gromacs-hbdons/10186 "2024-09-18T09:46:37Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hello how can i generate a result of the graphic A on Gromacs, If you know the command please reply with it. Mostly to be able to generate the aa i… --- ## [Inconsistency of gmx hbond analysis](https://gromacs.bioexcel.eu/t/inconsistency-of-gmx-hbond-analysis/8785)
**Author:** [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Replies:** 0\ **Last updated:** [April 4, 2024, 1:58pm UTC](https://gromacs.bioexcel.eu/t/inconsistency-of-gmx-hbond-analysis/8785 "2024-04-04T13:58:49Z")
GROMACS version: 2024 GROMACS modification: No I am running some hbond analysis because I want to take a look at the interactions between an arginine (ARG) in a protein and a lipid bilayer with two lipid types, cardiol… --- ## [Generate Histogram of HBonds](https://gromacs.bioexcel.eu/t/generate-histogram-of-hbonds/8461)
**Author:** [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)\ **Replies:** 0\ **Last updated:** [February 28, 2024, 6:21pm UTC](https://gromacs.bioexcel.eu/t/generate-histogram-of-hbonds/8461 "2024-02-28T18:21:56Z")
GROMACS version: 2022 GROMACS modification: No Hi, I need to generate a histogram with the number of water molecules making 1, 2, 3 or 4 hydrogen bonds with other water molecules. I thought about using gmx hbond for t… --- ## [Nature of H bonding in gromacs](https://gromacs.bioexcel.eu/t/nature-of-h-bonding-in-gromacs/8334)
**Author:** [@mohsen](https://gromacs.bioexcel.eu/u/mohsen)\ **Replies:** 4\ **Last updated:** [February 15, 2024, 12:34pm UTC](https://gromacs.bioexcel.eu/t/nature-of-h-bonding-in-gromacs/8334 "2024-02-15T12:34:13Z")
GROMACS version:2023 GROMACS modification: Yes/No What is the nature of H-bonding in GROMACS ? Is it primarily electrostatic , or does it calculate the number of H-bonds based on the angle and distance criteria? Can i… --- ## [H-bond calculation](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124)
**Author:** [@samapika](https://gromacs.bioexcel.eu/u/samapika)\ **Replies:** 3\ **Last updated:** [September 4, 2023, 9:18am UTC](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124 "2023-09-04T09:18:06Z")
GROMACS version:2020.2 GROMACS modification: No I am calculating the number of H-bond and ACF of H-bond using gmx hbond command. I have a bilayer which I have divided into bins along the z axis as: Interface region, Hy… --- ## [Gromacs hbond problem - 1 frame with high number of hbonds](https://gromacs.bioexcel.eu/t/gromacs-hbond-problem-1-frame-with-high-number-of-hbonds/7002)
**Author:** [@Davidb](https://gromacs.bioexcel.eu/u/Davidb)\ **Replies:** 2\ **Last updated:** [August 14, 2023, 7:48am UTC](https://gromacs.bioexcel.eu/t/gromacs-hbond-problem-1-frame-with-high-number-of-hbonds/7002 "2023-08-14T07:48:00Z")
GROMACS version: 2023 GROMACS modification: Yes - with plumed Hi, I am trying to analyze hbonds between a molecule and a protein. The complex was generated using CHARM-GUI so there is .itp file for the molecule. I am… --- ## [Hb Lifetime distribution calculation](https://gromacs.bioexcel.eu/t/hb-lifetime-distribution-calculation/6908)
**Author:** [@Abdulkareem](https://gromacs.bioexcel.eu/u/Abdulkareem)\ **Replies:** 1\ **Last updated:** [August 3, 2023, 8:12am UTC](https://gromacs.bioexcel.eu/t/hb-lifetime-distribution-calculation/6908 "2023-08-03T08:12:35Z")
GROMACS version: 2020.6 GROMACS modification: Yes/No I tried to calculate the hydrogen bond life time distribution using gmx module hbond with -life flag. The result I obtained is attached here , how to interpret thi… --- ## [Hydrogen bond profile](https://gromacs.bioexcel.eu/t/hydrogen-bond-profile/6644)
**Author:** [@Dev](https://gromacs.bioexcel.eu/u/Dev)\ **Replies:** 0\ **Last updated:** [June 20, 2023, 12:34pm UTC](https://gromacs.bioexcel.eu/t/hydrogen-bond-profile/6644 "2023-06-20T12:34:46Z")
GROMACS version: 2020.1 GROMACS modification: Yes with plumed Dear Users, I am trying to calculate the hydrogen bond profile between two groups ( donor and acceptor) based on the standard geometric conditions. I want …