# Average hydrogen-bonds calculation **URL:** \ **Category:** User discussions\ **Created:** [April 2, 2021, 12:29am UTC](https://gromacs.bioexcel.eu/t/average-hydrogen-bonds-calculation/1879 "2021-04-02T00:29:32Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![pkd675](https://avatars.discourse-cdn.com/v4/letter/p/ac91a4/32.png) [@pkd675](https://gromacs.bioexcel.eu/u/pkd675)\ **Post date:** [April 2, 2021, 12:29am UTC](https://gromacs.bioexcel.eu/t/average-hydrogen-bonds-calculation/1879/1 "2021-04-02T00:29:32Z")
GROMACS version: gmx hbond, version 2020.1-Ubuntu-2020.1-1 GROMACS modification: Yes/No I am doing the calculation Average Number of Hydrogen Bonds for Asphaltene-Asphaltene and Asphaltene-Polymar. I found results for some of the case (ANO\_PNT\_PVC) & (ASO\_AOH\_PNT\_PVC) but found the below error for this case (ANO\_ASO\_AOH\_PNT). I have zero knowledge to tackle this. Would anyone please suggest the best way to resolve this (step-by-step methodology is good for me)? The problem is below: Command line: gmx hbond -f md\_1.xtc -s md\_1.tpr -n Index.ndx -num hydrogenbonds.xvg -tu ns -b 0 -e 40 ## Reading file md\_1.tpr, VERSION 2019.3 (single precision) Note: file tpx version 116, software tpx version 119 Specify 2 groups to analyze: Group 0 ( System) has 353432 elements Group 1 ( Other) has 353432 elements Group 2 ( ANO) has 5450 elements Group 3 ( ASO) has 2950 elements Group 4 ( AOH) has 2975 elements Group 5 ( PNT) has 342057 elements Group 6 ( ANO\_ASO) has 8400 elements Group 7 ( ANO\_ASO\_AOH) has 11375 elements Group 8 (ANO\_ASO\_AOH\_PNT) has 353432 elements Select a group: 6 Selected 6: ‘ANO\_ASO’ Select a group: 6 Selected 6: ‘ANO\_ASO’ Calculating hydrogen bonds in ANO\_ASO (8400 atoms) Found 50 donors and 125 acceptors Reading frame 0 time 0.000 Will do grid-search on 67x67x67 grid, rcut=0.34999999 Frame loop parallelized with OpenMP using 8 threads. Reading frame 7 time 0.070 Program: gmx hbond, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxana/gmx\_hbond.cpp (line 980) Fatal error: Your computational box has shrunk too much. gmx hbond can not handle this situation, sorry. For more information and tips for troubleshooting, please check the GROMACS website at [Errors - Gromacs](http://www.gromacs.org/Documentation/Errors)