Dear Felix, Thanks for suggestions. I will try it now.
On Thu, Mar 29, 2012 at 5:40 PM, Rausch, Felix <frau...@ipb-halle.de> wrote: > Hello,**** > > ** ** > > The results of the energy minimization look reasonable. Nevertheless, you > should (visually) check your equilibration starting structure for problems > (e.g. clashes that could not be solved by EM). It would be a good idea to > concentrate on the atom numbers given in the error messages.**** > > ** ** > > To prevent the “exploding” system during equilibration, reducing the time > step may be a good idea. Or you could start with a short NVT run first to > equilibrate the temperature before switching to NPT. Furthermore, the > coupling of ions in a single thermostat group is in general not a good idea > (search the mailing list for many discussions about this topic).**** > > ** ** > > Good luck.**** > > ** ** > > *Von:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > *Im Auftrag von *Hendry > *Gesendet:* Donnerstag, 29. März 2012 11:25 > *An:* Discussion list for GROMACS users > *Betreff:* [gmx-users] Not able to continue with Equilibration**** > > ** ** > > 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**** > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. 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