[gmx-users] LINCS WARNING

Sun Iba sun.iba2 at gmail.com
Tue Jul 14 09:07:04 CEST 2015


Hello Everyone
I am simulation a protein as per the lysozyme tutorial. MY simulation got
dumped at final mdrun step. It is showing following warning :

Command line:
  gmx mdrun -deffnm md_0_1

Reading file md_0_1.tpr, VERSION 5.0.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
starting mdrun 'AMYLOID BETA A4 PROTEIN'
500000 steps,   2500.0 ps.

Step 166, time 0.83 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000162, max 0.000714 (between atoms 158 and 159)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    628    629   30.0    0.1090   0.1090      0.1090

Step 170, time 0.85 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000234, max 0.005085 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    623    624   73.1    0.1090   0.1084      0.1090
    628    629   55.1    0.1090   0.1089      0.1090

Step 171, time 0.855 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023399, max 1.013176 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    623    624   89.9    0.1084   0.2194      0.1090
Wrote pdb files with previous and current coordinates

Step 172, time 0.86 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000453, max 0.015917 (between atoms 628 and 629)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    623    624   44.8    0.2194   0.1084      0.1090
    628    629   75.5    0.1093   0.1073      0.1090

Step 173, time 0.865 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.639970, max 23.410875 (between atoms 628 and 629)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    619    621   30.3    0.1339   0.1284      0.1335
    621    622   46.9    0.1013   0.1019      0.1010
    623    624   89.7    0.1084   1.7118      0.1090
    623    625   72.5    0.1530   0.2719      0.1529
    623    638   43.1    0.1525   0.1587      0.1522
    625    626   46.9    0.1091   0.1372      0.1090
    625    627   61.5    0.1093   0.1643      0.1090
    625    628   89.3    0.1530   0.3458      0.1529
    628    629   90.0    0.1073   2.6608      0.1090
    628    630   74.1    0.1531   0.2413      0.1529
    628    634   88.3    0.1530   0.2401      0.1529
    634    635   41.2    0.1091   0.1433      0.1090
    634    636   38.2    0.1091   0.1357      0.1090
    634    637   39.0    0.1091   0.1380      0.1090
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 623 and 629
at distance 2.823 which is larger than the table limit 2.042 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



Step 174, time 0.87 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.212190, max 85.046806 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    260    263   90.0    0.1090   0.3693      0.1090
    621    622   70.2    0.1019   0.1815      0.1010
    621    623   41.5    0.1556   0.2046      0.1449
    623    624   90.5    1.7119   9.3791      0.1090
    623    625  126.5    0.2719   0.4357      0.1529
    623    638   62.1    0.1587   0.1499      0.1522
    625    626   96.2    0.1372   3.6085      0.1090
    625    627  115.3    0.1643   0.8026      0.1090
    625    628  115.4    0.3458   1.3529      0.1529
    628    630  125.4    0.2413   0.8808      0.1529
    628    634  147.0    0.2401   0.6961      0.1529
    630    633  134.3    0.0801   0.0868      0.1090
    634    635  118.3    0.1433   0.3006      0.1090
    634    636   77.6    0.1357   0.2433      0.1090
    634    637   56.3    0.1380   0.1960      0.1090
    638    640   33.7    0.1388   0.0773      0.1335
Wrote pdb files with previous and current coordinates

Step 175, time 0.875 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 14884.476208, max 642183.562500 (between atoms 634 and 636)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    227    229   30.3    0.1090   0.1118      0.1090
    234    236   90.0    0.1090   1.5776      0.1090
    249    250   89.9    0.1090   0.4785      0.1090
    254    255   48.8    0.1094   0.1421      0.1090
    254    260   73.2    0.1518   0.1647      0.1529
    260    261   89.8    0.1080   0.1514      0.1090
    260    262   53.0    0.1072   0.0889      0.1090
    260    263   90.0    0.3693   3.7940      0.1090
    414    430   30.9    0.1522   0.1901      0.1522
    430    431   35.4    0.1229   0.1618      0.1229
    430    432   64.5    0.1335   0.3594      0.1335
    432    433   64.8    0.1010   0.2799      0.1010
    432    434   79.9    0.1449   2.1805      0.1449
    434    435   76.2    0.1090   1.8989      0.1090
    434    436   80.5    0.1529   2.2481      0.1529
    436    437   72.6    0.1090   0.3409      0.1090
    436    438   75.4    0.1090   0.3557      0.1090
    436    439   76.4    0.1510   0.4095      0.1510
    439    440   31.7    0.1400   0.1724      0.1400
    439    442   30.5    0.1400   0.1720      0.1400
    450    451   69.2    0.1229   4.4884      0.1229
    450    452  102.9    0.1335   5.8859      0.1335
    452    453  109.5    0.1010   7.3353      0.1010
    452    454   69.7    0.1449  23.9641      0.1449
    454    455   90.0    0.1090 5368.6567      0.1090
    454    456   81.6    0.1529  33.5415      0.1529
    454    460   93.4    0.1523  37.3517      0.1522
    456    457   70.9    0.1090   5.0627      0.1090
    456    458   61.9    0.1090   3.8168      0.1090
    456    459  102.2    0.1090   5.7836      0.1090
    460    461   40.9    0.1229   1.5634      0.1229
    460    462   53.3    0.1336   1.9428      0.1335
    462    463   65.8    0.1010   1.1614      0.1010
    462    464   71.5    0.1449   1.6248      0.1449
    464    465   88.1    0.1090   0.7656      0.1090
    464    466   89.2    0.1529   0.8182      0.1529
    464    475   93.0    0.1523   0.7594      0.1522
    466    467  101.4    0.1090   0.0947      0.1090
    466    468  101.3    0.1090   0.1009      0.1090
    466    469  110.4    0.1529   0.0269      0.1529
    469    470   32.8    0.1090   0.1201      0.1090
    469    471   32.2    0.1090   0.1230      0.1090
    475    476   96.5    0.1229   0.0997      0.1229
    475    477   72.7    0.1336   0.0968      0.1335
    614    616   82.7    0.1450   0.5985      0.1449
    616    617   62.9    0.1124   0.5433      0.1090
    616    618   60.7    0.1113   0.5263      0.1090
    616    619  131.0    0.1581   1.9528      0.1522
    619    620  143.6    0.1222   2.0961      0.1229
    619    621   80.8    0.1286   4.0393      0.1335
    621    622  125.7    0.1815   2.3337      0.1010
    621    623  138.9    0.2046  53.3020      0.1449
    623    624  106.6    9.3791  45.5314      0.1090
    623    625  156.2    0.4357 109.0570      0.1529
    623    638  114.3    0.1499  52.1083      0.1522
    625    626   48.8    3.6085  68.8250      0.1090
    625    627   92.9    0.8026 2209.3792      0.1090
    625    628  137.6    1.3529 508.2758      0.1529
    628    629   48.4    3.1115 597.5058      0.1090
    628    630  129.9    0.8808 526.6873      0.1529
    628    634  113.7    0.6961 725.4713      0.1529
    630    631  143.0    0.1717 107.6285      0.1090
    630    633  123.8    0.0868  92.9717      0.1090
    634    635   80.1    0.3006 603.7111      0.1090
    634    636   89.9    0.2433 69998.1172      0.1090
    634    637   95.8    0.1960 801.4825      0.1090
    638    639  127.0    0.1129   4.0447      0.1229
    638    640   69.8    0.0773   3.4684      0.1335
    640    641  128.1    0.1165   0.6814      0.1010
    640    642  171.2    0.1593   0.5755      0.1449
    642    643   65.4    0.1112   0.1508      0.1090
    642    644   55.0    0.1554   0.2315      0.1529
    642    655   60.3    0.1542   0.2152      0.1522
    644    645   50.3    0.1096   0.1809      0.1090
    644    646   44.7    0.1098   0.1653      0.1090
    644    647   44.0    0.1536   0.2295      0.1529
    655    656   38.8    0.1243   0.1729      0.1229
    655    657   33.4    0.1351   0.1831      0.1335
    667    670   89.9    0.1090   0.1255      0.1090
    969    970   30.5    0.1010   0.1239      0.1010
    969    971   63.3    0.1450   0.2427      0.1449
    971    972   76.0    0.1090   0.1493      0.1090
    971    973   62.5    0.1530   0.1944      0.1529
    971    986   80.5    0.1523   0.2786      0.1522
    973    974   43.6    0.1090   0.1573      0.1090
    973    975   34.3    0.1529   0.1957      0.1529
    973    978   33.0    0.1529   0.1936      0.1529
    986    987   88.7    0.1230   0.1691      0.1229
    986    988   73.2    0.1336   1.1711      0.1335
    988    989   82.4    0.1010   0.8905      0.1010
    988    990   94.1    0.1449   4.5941      0.1449
    990    991   92.4    0.1090   3.6153      0.1090
    990    992   89.2    0.1090   4.4437      0.1090
    990    993  122.1    0.1522   4.7008      0.1522
    993    994   63.2    0.1229   3.2925      0.1229
    993    995   91.4    0.1335  76.0747      0.1335
    995    996   70.0    0.1010  36.9290      0.1010
    995    997   94.7    0.1449  32.1642      0.1449
    997    998   95.9    0.1090  47.8458      0.1090
    997    999   89.0    0.1529  54.3625      0.1529
    997   1012   94.0    0.1522  54.9975      0.1522
    999   1000  106.2    0.1090   5.1576      0.1090
    999   1001   89.6    0.1090   3.2550      0.1090
    999   1002  115.5    0.1529   3.0027      0.1529
   1002   1003   96.5    0.1090   2.6330      0.1090
   1002   1004   95.8    0.1529   2.8101      0.1529
   1002   1008   96.2    0.1529   2.8071      0.1529
   1004   1005   95.3    0.1090   0.3827      0.1090
   1004   1006   99.1    0.1090   0.3709      0.1090
   1004   1007   97.6    0.1090   0.3813      0.1090
   1008   1009   93.0    0.1090   0.4019      0.1090
   1008   1010   97.6    0.1090   0.3904      0.1090
   1008   1011  101.3    0.1090   0.3549      0.1090
   1012   1013   64.8    0.1229   3.2460      0.1229
   1012   1014   40.2    0.1335   2.6955      0.1335
   1014   1015  102.5    0.1010   3.2614      0.1010
   1014   1016  103.9    0.1449   3.5885      0.1449
   1016   1017   98.7    0.1090   1.0354      0.1090
   1016   1018   99.1    0.1529   0.9792      0.1529
   1016   1029   98.5    0.1522   1.0021      0.1522
   1018   1019   56.3    0.1090   0.0351      0.1090
   1018   1020  129.4    0.1090   0.0569      0.1090
   1029   1030   31.0    0.1229   0.0621      0.1229
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)

*Can anyone suggest what to do next*


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