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 version I get a note (but no warning or error) and then a segmentation fault, whereas when I supply a trajectory generated with the same version I get either:
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Program: gmx hbond, version 2023.1
Memory allocation failed:
std::bad_alloc
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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Hi Michele,
Thank you for reporting. Maybe a memory allocation problem. I have run some test with the option -num on my local machine. I did not have encounter any error. I did not run any test for -lifetime. Does the option -lifetime work for gmx hbond in GROMACS 2022?
You can report the issue on GitLab or/and test the new implementation of hbond. Note There is working going on to new version of gmx hbond on Gitlab see merge request Merge requests · GROMACS / GROMACS · GitLab
Note that the new tool is called hbond2
It will be great if you could test for your case and give feedback to the authors.
I am not sure that the option -lifetime is implemented, in case it is not I feel that it is important option to have. Please ask if it is possible
Thank you for the help
Alessandra
I assume the definition of lifetime that the -life option uses is not very useful. I can’t find any definition in the help text though (which by itself is already an issue).
Doing autocorrelation according to the theory of Luzar and Chandler.
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Program: gmx hbond, version 2023-flow_field-dev
Source file: src/gromacs/correlationfunctions/manyautocorrelation.cpp (line 61)
Function: int many_auto_correl(std::vector<std::vector<float> >*)
Inconsistency in user input:
Empty vector supplied
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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But I guess this is just because the arrays for output of gmx hbond were not initialized, I’ll try the fixed code.
I also got crazy numbers when I used gmx hbond in 2023.1, like “Average number of hbonds per timeframe -640700.743 out of 2875 possible”. I am running simulations for my study, should I install earlier version to obtain correct results?
I seem to still be having this problem. I tried both gmx hbond from Gromacs 2023.3 and gmx hbond-legacy from Gromacs 2025.1 and the output is the same:
Command line:
gmx hbond-legacy -f md.xtc -s md.tpr -ac
Reading file md.tpr, VERSION 2023.3 (single precision)
Note: file tpx version 129, software tpx version 137
You are going to use a deprecated gmx tool. Please migrate to the new one, gmx hbondSpecify 2 groups to analyze:
Group 0 ( System) has 329231 elements
Group 1 ( RNA) has 4253 elements
Group 2 ( CA) has 10 elements
Group 3 ( CL) has 337 elements
Group 4 ( MG) has 4 elements
Group 5 ( NA) has 441 elements
Group 6 ( Water) has 324186 elements
Group 7 ( SOL) has 324186 elements
Group 8 ( non-Water) has 5045 elements
Group 9 ( Ion) has 792 elements
Group 10 ( Water_and_ions) has 324978 elements
Select a group: 1
Selected 1: 'RNA'
Select a group: 1
Selected 1: 'RNA'
Calculating hydrogen bonds in RNA (4253 atoms)
Found 307 donors and 1431 acceptors
Making hbmap structure...done.
Reading frame 0 time 0.000
Will do grid-search on 39x39x28 grid, rcut=0.34999999
Segmentation fault (core dumped)
Any advice on if there’s a way to get H-bond lifetimes with recent versions of Gromacs. It looks like the post 2024 hbond doesn’t do lifetime analysis anymore?