[gmx-users] Segmentation fault, core dumped error

[Najamuddin Memon]

Instead of .trr file you can use .tpr and .xtc file


On Wed, May 29, 2019, 10:25 PM Neena Susan Eappen <
neena.susaneappen at mail.utoronto.ca> wrote:

> Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr
>
> Specify 2 groups to analyze:
>
> Group     0 (System) has   130 elements
>
> Group     1 (Protein) has   130 elements
>
> Group     2 (Protein-H) has    63 elements
>
> Group     3 (C-alpha) has    11 elements
>
> Group     4 (Backbone) has    34 elements
>
> Group     5 (MainChain) has    47 elements
>
> Group     6 (MainChain+Cb) has    58 elements
>
> Group     7 (MainChain+H) has    58 elements
>
> Group     8 (SideChain) has    72 elements
>
> Group     9 (SideChain-H) has    16 elements
>
>
> Select a group: 1 Selected 1: 'Protein'
>
> Select a group: 1 Selected 1: 'Protein'
>
> Output: Calculating hydrogen bonds in Protein (130 atoms)
>
> Found 13 donors and 25 acceptors
>
> trr version: GMX_trn_file (single precision)
>
> Reading frame       0 time    0.000
>
> Will do grid-seach on 2374x2374x2374 grid, rcut=0.35
>
> Segmentation fault (core dumped)
>
> ________________________________
> From: Neena Susan Eappen
> Sent: Tuesday, May 28, 2019 11:31 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Segmentation fault, core dumped error
>
> Hello gromacs users,
>
> Is there a reason why segmentation fault appeared when gmx hbond command
> was used?
>
> Thank you,
> Neena
>
> ________________________________
> From: Neena Susan Eappen
> Sent: Friday, May 24, 2019 12:40 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Segmentation fault, core dumped error
>
> Hello gromacs users,
>
> I got an error message when I used gmx hbond command: Segmentation fault,
> core dumped. Shown below is my gmx version details (if that can point to my
> problem). Any insight would be appreciated.
>
> GROMACS version:        2018.4
> Precision:      single
> Memory model:   64 bit
> MPI library:    thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
> GPU support:    disabled
> SIMD instructions:      AVX2_256
> FFT library:    fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
> RDTSCP usage:   enabled
> TNG support:    enabled
> Hwloc support:  disabled
> Tracing support:        disabled
> Built on:       2019-01-12 0:35
> Built by:       name at HP-PC [CMAKE]<mailto:name at HP-PC%20[CMAKE]>
> Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
> Build CPU vendor:       Intel
> Build CPU brand:        Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
> Build CPU family:       6   Model: 61   Stepping: 4
> Build CPU features:     aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler:     /usr/bin/cc GNU 7.3.0
> C compiler flags:       march=core-AVX2     -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
> C++ compiler:   /usr/bin/c++ GNU 7.3.0
> C++ compiler flags:     -march=core-avx2    -std=c++11   -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
>
> Thank you,
> Neena
> --
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