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