# GMX hbond generating weird result **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools, gmx-hbond\ **Created:** [January 6, 2025, 12:43pm UTC](https://gromacs.bioexcel.eu/t/gmx-hbond-generating-weird-result/10951 "2025-01-06T12:43:00Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [January 6, 2025, 12:43pm UTC](https://gromacs.bioexcel.eu/t/gmx-hbond-generating-weird-result/10951/1 "2025-01-06T12:43:00Z")
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 hbond.log -num hbnum.xvg Output: :-) GROMACS - gmx hbond, 2023 (-: Executable: /home/adglab/Desktop/GROMACS/gromacs-2023/build/bin/gmx Data prefix: /home/adglab/Desktop/GROMACS/gromacs-2023 (source tree) Working dir: /home/adglab/Gromacs\_trial\_run/Analysis/H-bond\_100ns Command line: gmx hbond -f md\_0\_100\_center.xtc -s md\_0\_100.tpr -tu ns -g hbond.log -num hbnum.xvg Reading file md\_0\_100.tpr, VERSION 2023 (single precision) Specify 2 groups to analyze: Group 0 ( System) has 54575 elements Group 1 ( Protein) has 5570 elements Group 2 ( Protein-H) has 2765 elements Group 3 ( C-alpha) has 345 elements Group 4 ( Backbone) has 1035 elements Group 5 ( MainChain) has 1379 elements Group 6 ( MainChain+Cb) has 1708 elements Group 7 ( MainChain+H) has 1699 elements Group 8 ( SideChain) has 3871 elements Group 9 ( SideChain-H) has 1386 elements Group 10 ( Prot-Masses) has 5570 elements Group 11 ( non-Protein) has 49005 elements Group 12 ( Other) has 34 elements Group 13 ( LIG1) has 34 elements Group 14 ( CL) has 8 elements Group 15 ( Water) has 48963 elements Group 16 ( SOL) has 48963 elements Group 17 ( non-Water) has 5612 elements Group 18 ( Ion) has 8 elements Group 19 ( Water\_and\_ions) has 48971 elements Select a group: 1 Selected 1: ‘Protein’ Select a group: 13 Selected 13: ‘LIG1’ Checking for overlap in atoms between Protein and LIG1 Calculating hydrogen bonds between Protein (5570 atoms) and LIG1 (34 atoms) Found 504 donors and 979 acceptors Reading frame 0 time 0.000 Will do grid-search on 21x21x15 grid, rcut=0.34999999 Frame loop parallelized with OpenMP using 48 threads. Last frame 10000 time 100.000 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.1# Average number of hbonds per timeframe -832023.980 out of 246708 possible GROMACS reminds you: “UNIX is basically a simple operating system. It just takes a genius to understand its simplicity.” (Dennis Ritchie) While, I analysed the H-bonds using VMD, which gives a nice plot like this, ![Screenshot from 2025-01-06 15-24-56](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/30305b934cdfbb176572bf50f848968dbf832f29.png), using the same files (gro and xtc files in this case). Any explanation what might have gone wrong in my case? My simulation stopped at 97.78 ns due to power cut, which I resumed later on by adding -cpi to this, “gmx mdrun -deffnm md\_0\_100” command. Is this why the problem is appearing? Same tpr and xtc file I have used to generate RMSD and RMSF plot, which ran successfully and have the desired patterns. I have previously run a 2ns trial run, for which there was no problem as such. This is the same protein-ligand molecule I’m running, just for a higher time duration. GROMACS version is: :-) GROMACS - gmx, 2023 (-: Executable: /home/adglab/Desktop/GROMACS/gromacs-2023/build/bin/gmx Data prefix: /home/adglab/Desktop/GROMACS/gromacs-2023 (source tree) Working dir: /home/adglab/Gromacs\_trial\_run/Analysis/H-bond\_100ns Command line: gmx --version GROMACS version: 2023 Precision: mixed Memory model: 64 bit MPI library: thread\_mpi OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 128) GPU support: CUDA NB cluster size: 8 SIMD instructions: AVX\_512 CPU FFT library: fftw-3.3.10-sse2-avx GPU FFT library: cuFFT Multi-GPU FFT: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/cc GNU 13.3.0 C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw -Wno-missing-field-initializers -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 13.3.0 C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw -Wno-missing-field-initializers -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG BLAS library: LAPACK library: CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2024 NVIDIA Corporation;Built on Tue\_Oct\_29\_23:50:19\_PDT\_2024;Cuda compilation tools, release 12.6, V12.6.85;Build cuda\_12.6.r12.6/compiler.35059454\_0 CUDA compiler flags:-std=c++17;–generate-code=arch=compute\_50,code=sm\_50;–generate-code=arch=compute\_52,code=sm\_52;–generate-code=arch=compute\_60,code=sm\_60;–generate-code=arch=compute\_61,code=sm\_61;–generate-code=arch=compute\_70,code=sm\_70;–generate-code=arch=compute\_75,code=sm\_75;–generate-code=arch=compute\_80,code=sm\_80;–generate-code=arch=compute\_86,code=sm\_86;–generate-code=arch=compute\_89,code=sm\_89;–generate-code=arch=compute\_90,code=sm\_90;-Wno-deprecated-gpu-targets;–generate-code=arch=compute\_53,code=sm\_53;–generate-code=arch=compute\_80,code=sm\_80;-use\_fast\_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;-D\_FORCE\_INLINES;-fexcess-precision=fast -funroll-all-loops -mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw -Wno-missing-field-initializers -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG CUDA driver: 0.0 CUDA runtime: 12.60 GROMACS modifications: No ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 7, 2025, 2:05am UTC](https://gromacs.bioexcel.eu/t/gmx-hbond-generating-weird-result/10951/2 "2025-01-07T02:05:58Z")
> [@nilanjana88](#): > > Any explanation what might have gone wrong in my case? Nothing, judging by this output. Hydrogen bonds are a discrete quantity so they take only integer values. It looks strange to plot them in XmGrace with a line connecting the points, but if you remove the line and just plot the data points, it makes a lot more sense (visually). ---
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [January 7, 2025, 6:16am UTC](https://gromacs.bioexcel.eu/t/gmx-hbond-generating-weird-result/10951/3 "2025-01-07T06:16:30Z")
But doesn’t it seem suspicious that average number of hydrogen bonds per timeframe is negative? I never got average hydrogen bonds in negative for the same pair of protein-ligand. It is a well-known inhibitor for this protein (GSK3β in this case), which has been shown to form at least 3 hydrogen bonds when bound to the active site of this protein. ---
**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\ **Post date:** [January 7, 2025, 6:29am UTC](https://gromacs.bioexcel.eu/t/gmx-hbond-generating-weird-result/10951/4 "2025-01-07T06:29:00Z")
Also, when I’m trying to generate the hbmap.xpm file using “-hbm” flag, it gives some error. Command line: gmx hbond -s md\_0\_100.tpr -f md\_0\_100\_center.xtc -hbn hbond.ndx -hbm hbmap.xpm Reading file md\_0\_100.tpr, VERSION 2023 (single precision) Specify 2 groups to analyze: Group 0 ( System) has 54575 elements Group 1 ( Protein) has 5570 elements Group 2 ( Protein-H) has 2765 elements Group 3 ( C-alpha) has 345 elements Group 4 ( Backbone) has 1035 elements Group 5 ( MainChain) has 1379 elements Group 6 ( MainChain+Cb) has 1708 elements Group 7 ( MainChain+H) has 1699 elements Group 8 ( SideChain) has 3871 elements Group 9 ( SideChain-H) has 1386 elements Group 10 ( Prot-Masses) has 5570 elements Group 11 ( non-Protein) has 49005 elements Group 12 ( Other) has 34 elements Group 13 ( LIG1) has 34 elements Group 14 ( CL) has 8 elements Group 15 ( Water) has 48963 elements Group 16 ( SOL) has 48963 elements Group 17 ( non-Water) has 5612 elements Group 18 ( Ion) has 8 elements Group 19 ( Water\_and\_ions) has 48971 elements Select a group: 1 Selected 1: ‘Protein’ Select a group: 13 Selected 13: ‘LIG1’ Checking for overlap in atoms between Protein and LIG1 Calculating hydrogen bonds between Protein (5570 atoms) and LIG1 (34 atoms) Found 504 donors and 979 acceptors Making hbmap structure…done. Reading frame 0 time 0.000 Will do grid-search on 21x21x15 grid, rcut=0.34999999 Frame loop parallelized with OpenMP using 48 threads. Last frame 10000 time 100000.000 Found 35 different hydrogen bonds in trajectory Found 59 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 233/504Segmentation fault (core dumped) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 7, 2025, 5:47pm UTC](https://gromacs.bioexcel.eu/t/gmx-hbond-generating-weird-result/10951/5 "2025-01-07T17:47:07Z")
Something seems buggy. Can you try version 2024.4?