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: [email protected] 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: [email protected] 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@HP-PC [CMAKE]<mailto:name@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 [email protected].
