Hi,
I am using Gromacs 4.5.4. After successful minimization by SD, I continued with equilibration step but I got the below errors. I tried many times with different parameters but the problem still persists. I have given errors and md parameters of equilibration step below. I have also provided my minimization output at the end. Could you provide some suggestions what went wrong?. Many thanks Sincerely Hendry *Errors:* Warning: 1-4 interaction between 2969 and 2974 at distance 5.543 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 92.242942, max 9194.071289 (between atoms 3025 and 3024) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2987 2973 106.3 1.3892 7.3433 0.1530 2974 2973 174.8 1.1940 7.7482 0.1530 2975 2974 79.9 0.1865 1.4460 0.1530 2978 2975 98.5 0.1423 0.6164 0.1390 2982 2978 86.1 0.1421 0.6512 0.1390 2979 2978 89.8 0.1114 5.2456 0.1090 2989 2987 132.2 0.1781 2.6697 0.1330 2988 2987 142.2 0.2284 2.7180 0.1230 2971 2969 62.9 7.0921 3.5084 0.1330 2970 2969 88.1 6.8598 4.7791 0.1230 2973 2971 120.6 2.8109 8.8274 0.1470 2972 2971 165.6 2.0293 6.9953 0.1000 3016 3013 103.1 0.5628 65.6450 0.1390 3014 3013 39.0 0.3331 5.0018 0.1330 3017 3014 81.6 0.1827 57.9252 0.1330 3015 3014 77.9 0.0752 6.3613 0.1090 3020 3016 81.3 2.2255 79.7378 0.1390 3019 3016 100.9 0.4862 54.4883 0.1390 3019 3017 79.3 0.1679 57.8415 0.1330 3018 3017 94.5 0.1686 66.3440 0.1000 3022 3019 87.7 0.5657 7.7539 0.1390 3026 3022 104.5 0.8085 54.9923 0.1390 3023 3022 87.4 0.6108 5.0641 0.1090 2968 2964 174.1 1.5617 5.1413 0.1470 2965 2964 59.5 5.2178 4.0658 0.1470 2969 2965 35.5 7.6693 2.9000 0.1530 2966 2965 137.3 5.3225 4.6157 0.1530 2967 2966 150.3 1.6016 1.7332 0.1530 2968 2967 72.4 0.1685 1.8310 0.1530 3026 3024 94.8 0.8572 96.6156 0.1390 3025 3024 89.9 0.6811 1002.2628 0.1090 3027 3026 108.0 1.1638 47.5384 0.1090 2991 2989 138.2 0.2045 0.6556 0.1470 2990 2989 157.0 0.1236 0.7213 0.1000 2998 2991 89.9 0.1961 0.9471 0.1530 2992 2991 79.5 0.1931 0.5434 0.1530 2993 2992 49.8 0.1577 0.1862 0.1530 3000 2998 84.9 0.1463 0.5492 0.1330 2999 2998 83.3 0.1346 0.5372 0.1230 3002 3000 44.2 0.1535 0.2150 0.1470 3003 3002 31.6 0.1548 0.1834 0.1530 3009 3007 62.4 0.1507 0.3181 0.1330 3008 3007 44.1 0.1280 0.1578 0.1230 3011 3009 80.3 0.2401 1.9894 0.1470 3010 3009 82.9 0.1141 0.3157 0.1000 3028 3011 85.2 0.2391 1.9233 0.1530 3012 3011 97.9 0.3034 4.9831 0.1530 3013 3012 82.4 0.3759 7.3991 0.1530 3024 3020 85.6 2.4674 98.3412 0.1390 3021 3020 81.0 1.2452 66.1375 0.1090 3030 3028 88.9 0.1492 0.2673 0.1330 3029 3028 61.2 0.1379 0.2407 0.1230 49372 49371 89.5 0.1000 221.0566 0.1000 49373 49371 92.4 0.1000 170.7231 0.1000 2956 2954 153.4 0.1550 3.5621 0.1470 2955 2954 135.5 0.1246 0.8967 0.1000 2962 2956 76.6 0.7151 5.0532 0.1530 2957 2956 178.7 0.1220 3.9773 0.1530 2958 2957 155.0 0.2036 1.2639 0.1530 2961 2959 34.5 0.1265 0.1186 0.1250 2960 2959 30.4 0.1264 0.1346 0.1250 2964 2962 114.9 1.7422 7.9205 0.1330 2963 2962 156.9 0.4832 6.1127 0.1230 53158 53157 90.0 0.1000 0.1575 0.1000 53159 53157 90.0 0.1000 0.1747 0.1000 53386 53385 90.0 0.1000 0.1537 0.1000 53387 53385 56.5 0.1000 0.0962 0.1000 2954 2952 68.7 0.1615 0.7870 0.1330 Back Off! I just backed up step1b_n2.pdb to ./#step1b_n2.pdb.1# Back Off! I just backed up step1c_n2.pdb to ./#step1c_n2.pdb.1# Wrote pdb files with previous and current coordinates ------------------------------------------------------- Program mdrun, VERSION 4.5.4 Source code file: pme.c, line: 538 Fatal error: 10 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "They Were So Quiet About It" (Pixies) Error on node 2, will try to stop all the nodes Halting parallel program mdrun on CPU 2 out of 4 gcq#37: "They Were So Quiet About It" (Pixies) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun has exited due to process rank 2 with PID 30681 on node ymu039-107 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). *Equilibration parameters* title = TM1 in a POPC bilayer at 100K cpp = /lib/cpp integrator = md define = -DPO1000 ; Output dt = 0.002 ; ps ! nsteps = 100000 ; total 200 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 500 xtc_precision = 1000 ; Electrostatics and VdW nstlist = 5 pbc = xyz rlist = 1.2 coulombtype = PME rcoulomb = 1.2 fourierspacing = 0.16 pme_order = 4 rvdw = 1.4 constraints = all-bonds optimize_fft = yes constraint-algorithm = lincs lincs-order = 4 lincs_iter = 1 ; berendsen temperature coupling Tcoupl = berendsen tc-grps = Protein POPC SOL CL tau_t = 0.1 0.1 0.1 0.1 ref_t = 100 100 100 100 ; Energy monitoring energygrps = Protein POPC SOL CL ; Isotropic pressure coupling pcoupl = parrinello-rahman pcoupltype = semiisotropic tau_p = 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; Generate velocity is on 100K gen_vel = yes gen_temp = 100.0 gen_seed = 173529 *SD minimization ouput:* Steepest Descents converged to Fmax < 1000 in 23239 steps Potential Energy = -1.0507182e+06 Maximum force = 9.8500549e+02 on atom 5087 Norm of force = 2.4736889e+01
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