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