[gmx-users] Not able to continue with Equilibration
Hendry
winterhot82 at gmail.com
Thu Mar 29 12:47:02 CEST 2012
Dear Felix,
Thanks for suggestions. I will try it now.
On Thu, Mar 29, 2012 at 5:40 PM, Rausch, Felix <frausch at 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-bounces at gromacs.org [mailto:gmx-users-bounces at 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****
>
> --
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