Floating Point Exception at H-Bond Analysis

User discussions
1

GROMACS version: 2023.3
GROMACS modification:
Here post your question

Dear all,

I’m getting this error while performing hydrogen bond analysis of the MD trajectory of my complex. I have browsed this error in the forum but could not get any clear solution.

                      :-) GROMACS - gmx hbond, 2023.3 (-:

Command line:
  gmx hbond -f md100ns-best.xtc -s md100ns.tpr -num hbnum.xvg -tu ns

Reading file md100ns.tpr, VERSION 2021.3 (single precision)
Note: file tpx version 122, software tpx version 129
Specify 2 groups to analyze:
Group     0 (         System) has 69491 elements
Group     1 (        Protein) has  4447 elements
Group     2 (      Protein-H) has  2231 elements
Group     3 (        C-alpha) has   274 elements
Group     4 (       Backbone) has   822 elements
Group     5 (      MainChain) has  1095 elements
Group     6 (   MainChain+Cb) has  1350 elements
Group     7 (    MainChain+H) has  1354 elements
Group     8 (      SideChain) has  3093 elements
Group     9 (    SideChain-H) has  1136 elements
Group    10 (    Prot-Masses) has  4447 elements
Group    11 (    non-Protein) has 65044 elements
Group    12 (          Other) has    52 elements
Group    13 (            LIG) has    51 elements
Group    14 (            CLA) has     1 elements
Group    15 (          Water) has 64992 elements
Group    16 (            SOL) has 64992 elements
Group    17 (      non-Water) has  4499 elements
Select a group: 1
Selected 1: 'Protein'
Select a group: 13
Selected 13: 'LIG'
Checking for overlap in atoms between Protein and LIG
Calculating hydrogen bonds between Protein (4447 atoms) and LIG (51 atoms)
Found 400 donors and 793 acceptors
Reading frame       0 time    0.000
Will do grid-search on 20x20x20 grid, rcut=0.34999999
Frame loop parallelized with OpenMP using 16 threads.
Reading frame     110 time    1.100   Floating point exception

Any help would be appreciated. Thanks in advance.

2

Hi!

Looks like a new bug. Could you share your input files? If the trajectory file is too large, you can cut it with gmx trjconv

3

Hi!

Unfortunately, I got the same error while trying to cut my trajectory file. Actually I calculated RMSD, RMSF, Rg and SASA etc. using this trajectory without any problems so I don’t think it’s broken or anything.

4

Can you then upload it somewhere? This is definitely a bug (not necessarily anything wrong with the trajectory, but, apparently, it has some property that is not handled well by some analysis tools). Unfortunately, without a way to reproduce it, we can hardly fix the problem.

If you cannot share the file, perhaps you can run your program under a debugger to get a stack trace? Roughly like this:

$ gdb --args gmx hbond -f md100ns-best.xtc -s md100ns.tpr -num hbnum.xvg -tu ns
[ten lines of boilerplate printed]
(gdb) run
[GROMACS starts running and crahes]
(gdb) bt
[It will print the trace to the error location here : that's what we need]
5

Here you can find the files in the links below:
Link for .tpr
Link for .xtc

6

you need to give the access to the files-“public”

7

Thanks. Interestingly, I don’t observe any crashes with either GROMACS 2023.3 or newer. What is the output of gmx -version and how did you install GROMACS?

8

Here is the output:

GROMACS version:    2023.3
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support:        disabled
SIMD instructions:  AVX2_256
CPU FFT library:    fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library:    none
Multi-GPU FFT:      none
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 11.4.0
C compiler flags:   -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 11.4.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
BLAS library:       Internal
LAPACK library:     Internal

Actually, I followed the default installation instruction without changing any parameters.

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