[gmx-users] Segmentation fault, core dumped error

[Najamuddin Memon]

You can go to gmx hbond tutorial in gromacs.


On Thu, May 30, 2019, 5:12 AM Najamuddin Memon <najamuddinmemon63 at gmail.com>
wrote:

> 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>