Hello all, I am minimizing a system of 2000 water molecules again but I have several error messages. Is my timestep too large indeed? The error message also mentions segmentation fault. I have only 6000 atoms in my system but the output shows atom 7783 and 8879. I'm not sure what's going on. My pdb file is shown below and the output of the minimization is written after the output. Please, help me locate the problem.
; VARIOUS PREPROCESSING OPTIONS title = NPT simulation of water cpp = /lib/cpp include = -I../top define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 5000 simulation_part = 1 init_step = 0 comm-mode = Linear nstcomm = 1 ; LANGEVIN DYNAMICS bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS emtol = 1000 emstep = 0.01 ; OUTPUT CONTROL OPTIONS nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 100 xtc-precision = 1000 xtc-grps = SOL energygrps = SOL ; ; PARAMETERS FOR NEIGHBORSEARCHING nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist = 0.9 ; ELECTROSTATICS AND VDW OPTIONS coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.4 DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.135 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes t = 4.066 ps: Water molecule starting at atom 1993 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 2034, Dmax= 3.4e-02 nm, Epot= 1.48017e+09 Fmax= 1.08293e+08, atom= 7783 Step= 2035, Dmax= 4.0e-02 nm, Epot= 1.46516e+09 Fmax= 1.83787e+09, atom= 1993 Step= 2037, Dmax= 2.4e-02 nm, Epot= 1.44351e+09 Fmax= 2.34469e+08, atom= 1993 Step= 2038, Dmax= 2.9e-02 nm, Epot= 1.42904e+09 Fmax= 4.29069e+08, atom= 1993 Step= 2039, Dmax= 3.5e-02 nm, Epot= 1.41457e+09 Fmax= 2.10114e+08, atom= 1993 Step= 2040, Dmax= 4.2e-02 nm, Epot= 1.39993e+09 Fmax= 3.01888e+08, atom= 1993 Step= 2042, Dmax= 2.5e-02 nm, Epot= 1.38636e+09 Fmax= 2.28092e+08, atom= 4549 Step= 2043, Dmax= 3.0e-02 nm, Epot= 1.37259e+09 Fmax= 1.40258e+08, atom= 4549 Step= 2044, Dmax= 3.6e-02 nm, Epot= 1.35660e+09 Fmax= 4.77136e+08, atom= 4549 Step= 2045, Dmax= 4.3e-02 nm, Epot= 1.34145e+09 Fmax= 1.32867e+08, atom= 4549 Step= 2047, Dmax= 2.6e-02 nm, Epot= 1.32970e+09 Fmax= 3.61866e+08, atom= 3097 Step= 2048, Dmax= 3.1e-02 nm, Epot= 1.31958e+09 Fmax= 3.14277e+08, atom= 3097 Step= 2049, Dmax= 3.7e-02 nm, Epot= 1.31567e+09 Fmax= 9.12713e+08, atom= 3964 Step= 2050, Dmax= 4.5e-02 nm, Epot= 1.30841e+09 Fmax= 6.21777e+08, atom= 3964 Step= 2051, Dmax= 5.4e-02 nm, Epot= 1.30480e+09 Fmax= 5.82421e+08, atom= 3637 t = 4.104 ps: Water molecule starting at atom 3637 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 2052, Dmax= 6.5e-02 nm, Epot= 1.29311e+09 Fmax= 4.72304e+08, atom= 3079 t = 4.106 ps: Water molecule starting at atom 3079 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 2054, Dmax= 3.9e-02 nm, Epot= 1.27930e+09 Fmax= 1.93571e+08, atom= 8879 Step= 2056, Dmax= 2.3e-02 nm, Epot= 1.26788e+09 Fmax= 3.64079e+08, atom= 1411 Step= 2057, Dmax= 2.8e-02 nm, Epot= 1.25869e+09 Fmax= 2.08411e+08, atom= 5857 Step= 2058, Dmax= 3.4e-02 nm, Epot= 1.24544e+09 Fmax= 1.25967e+08, atom= 5857 Step= 2060, Dmax= 2.0e-02 nm, Epot= 1.23279e+09 Fmax= 1.91600e+08, atom= 1411 Step= 2061, Dmax= 2.4e-02 nm, Epot= 1.22254e+09 Fmax= 1.33277e+08, atom= 88 Step= 2062, Dmax= 2.9e-02 nm, Epot= 1.20834e+09 Fmax= 1.80612e+08, atom= 1411 Step= 2063, Dmax= 3.5e-02 nm, Epot= 1.20371e+09 Fmax= 4.86526e+08, atom= 1411 Step= 2064, Dmax= 4.2e-02 nm, Epot= 1.20033e+09 Fmax= 8.14034e+08, atom= 5857 Step= 2065, Dmax= 5.0e-02 nm, Epot= 1.18726e+09 Fmax= 3.57392e+08, atom= 2851 Step= 2067, Dmax= 3.0e-02 nm, Epot= 1.18000e+09 Fmax= 3.11047e+08, atom= 2851 Step= 2068, Dmax= 3.6e-02 nm, Epot= 1.17184e+09 Fmax= 3.86104e+08, atom= 4048 Step= 2069, Dmax= 4.3e-02 nm, Epot= 1.16512e+09 Fmax= 3.59701e+08, atom= 4162 Step= 2070, Dmax= 5.2e-02 nm, Epot= 1.15932e+09 Fmax= 3.93044e+08, atom= 4162 Step= 2072, Dmax= 3.1e-02 nm, Epot= 1.14698e+09 Fmax= 6.99317e+07, atom= 2236 Step= 2073, Dmax= 3.7e-02 nm, Epot= 1.13498e+09 Fmax= 5.46620e+08, atom= 2236 Step= 2074, Dmax= 4.5e-02 nm, Epot= 1.11948e+09 Fmax= 5.85052e+08, atom= 4825 Step= 2075, Dmax= 5.4e-02 nm, Epot= 1.10614e+09 Fmax= 2.05211e+08, atom= 4162 t = 4.152 ps: Water molecule starting at atom 4162 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Segmentation fault Thank you, Lum
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