Hi, Gromacs users, I was caught by a big problem with molecular dynamic investigation of an cyclic peptide nanotube. When i do energy minimization with em.mdp parameter file as follows, it gave out a warning: Warning: 1-4 interaction between 135 and 144 at distance larger than 1 nm. I ignored it and went on the next step with pr.mdp as follows, but it crashed with the following information:
Wrote pdb files with previous and current coordinates [node1:15777] *** Process received signal *** [node1:15777] Signal: Segmentation fault (11) [node1:15777] Signal code: Address not mapped (1) [node1:15777] Failing at address: 0xba8e28 [node1:15777] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:15777] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58] [node1:15777] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97] [node1:15777] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:15777] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:15777] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:15777] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:15777] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:15777] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:15777] [ 9] mdrun_ompi [0x412e8a] [node1:15777] *** End of error message *** Segmentation fault I am extremely puzzed and don't know how to solve this problem. In additon, my previous system runs normally with the same parameter file. ##############em.mdp file cpp = /lib/cpp define = -DPOSRES constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no #########pr.mdp title = Yo cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 2500 ; total 5 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 5 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 pme_order = 4 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein tau_t = 0.1 ref_t = 10 ; Energy monitoring energygrps = Protein ; Pressure coupling is not on Pcoupl = berendsen pcoupltype = anisotropic tau_p = 1 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1 1 1 1 1 1 ; Generate velocites is on at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529 Look forward to your help. Thanks in advance. Huifang
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