[gmx-users] mdrun segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 28 23:35:36 CEST 2009
sunny mishra wrote:
> Dear all,
>
> At the final step of my mdrun I get LINCS warning. I don't know whats
> the issue. Please help me out.
>
>
If I had a nickel for every time I saw a LINCS warning on this list... :)
The answer is always the same. There is something physically unrealistic about
your simulation such that it is "blowing up." See here:
http://www.gromacs.org/WIKI-import/Blowing_Up
And the relevant entry here:
http://www.gromacs.org/WIKI-import/Main_Page/Errors
-Justin
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 51.050964, max 314.598846 (between atoms 3 and 4)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 51 52 90.0 0.2700 16.3676 0.2700
> 51 53 90.0 0.2700 17.4243 0.2700
> 52 53 90.2 0.2700 2.1691 0.2700
> 57 58 90.0 0.2700 19.9248 0.2700
> 57 59 90.0 0.2700 27.7437 0.2700
> 58 59 89.9 0.2700 9.5994 0.2700
> 67 68 89.1 0.2700 11.0711 0.2700
> 67 69 89.5 0.2700 17.3915 0.2700
> 68 69 89.1 0.2700 8.9722 0.2700
> 68 70 88.7 0.2700 7.4897 0.2700
> 69 70 89.1 0.2700 10.5427 0.2700
> 74 75 90.0 0.2700 15.9658 0.2700
> 74 76 90.0 0.2700 14.3261 0.2700
> 75 76 90.0 0.2700 15.3014 0.2700
> 78 79 53.0 0.2700 0.3682 0.2700
> 78 80 36.0 0.2700 0.2621 0.2700
> 79 80 78.8 0.2700 0.3108 0.2700
> 79 81 74.6 0.2700 0.2500 0.2700
> 96 97 90.0 0.2700 5.6881 0.2700
> 96 98 90.0 0.2700 12.4635 0.2700
> 97 98 90.0 0.2700 12.2473 0.2700
> 105 106 92.0 0.2700 5.3689 0.2700
> 105 107 90.9 0.2700 4.9643 0.2700
> 106 107 89.5 0.2700 5.2502 0.2700
> 106 108 90.2 0.2700 12.9074 0.2700
> 107 108 89.8 0.2700 13.3348 0.2700
> 123 124 90.0 0.2700 0.3295 0.2700
> 123 125 90.0 0.2700 0.4033 0.2700
> 124 125 90.0 0.2700 0.4582 0.2700
> 134 135 89.8 0.2700 7.5418 0.2700
> 134 136 89.8 0.2700 7.6180 0.2700
> 135 136 89.8 0.2700 7.5943 0.2700
> 177 178 90.0 0.2700 21.0157 0.2700
> 177 179 90.0 0.2700 21.3382 0.2700
> 178 179 90.0 0.2700 5.0506 0.2700
> 206 207 90.1 0.2700 3.7166 0.2700
> 206 208 90.0 0.2700 17.1633 0.2700
> 207 208 90.0 0.2700 14.3937 0.2700
> 210 211 90.0 0.2700 1.4919 0.2700
> 210 212 90.0 0.2700 1.4477 0.2700
> 229 230 89.9 0.2700 46.6891 0.2700
> 229 231 89.8 0.2700 12.4685 0.2700
> 230 231 89.9 0.2700 34.3535 0.2700
> 233 234 90.0 0.2700 17.0640 0.2700
> 233 235 90.0 0.2700 12.0837 0.2700
> 234 235 90.0 0.2700 21.1578 0.2700
> 240 241 90.1 0.2700 14.3404 0.2700
> 240 242 89.9 0.2700 5.5938 0.2700
> 241 242 89.5 0.2700 10.7072 0.2700
> 241 243 90.1 0.2700 11.1853 0.2700
> 242 243 89.9 0.2700 14.6316 0.2700
> 278 279 90.4 0.2700 0.4126 0.2700
> 278 280 90.3 0.2700 0.6367 0.2700
> 279 280 90.3 0.2700 0.6632 0.2700
> 321 322 90.1 0.2700 13.7866 0.2700
> 321 323 90.1 0.2700 8.6467 0.2700
> 322 323 90.1 0.2700 6.2637 0.2700
> 325 327 89.9 0.2700 5.2665 0.2700
> 326 327 89.9 0.2700 5.3472 0.2700
> 343 344 90.2 0.2700 5.8168 0.2700
> 343 345 90.5 0.2700 5.0440 0.2700
> 344 345 90.2 0.2700 5.9636 0.2700
> 344 346 89.7 0.2700 6.8436 0.2700
> 345 346 89.5 0.2700 2.4697 0.2700
> 364 365 89.9 0.2700 1.8601 0.2700
> 364 366 90.0 0.2700 2.8203 0.2700
> 365 366 89.9 0.2700 1.4138 0.2700
> 389 390 90.0 0.2700 0.4660 0.2700
> 389 391 90.0 0.2700 0.4625 0.2700
> 390 391 90.0 0.2700 0.4644 0.2700
> 417 418 89.9 0.2700 3.9010 0.2700
> 417 419 89.9 0.2700 3.8294 0.2700
> 418 419 51.6 0.2700 0.2606 0.2700
> 418 420 89.6 0.2700 0.5341 0.2700
> 419 420 89.7 0.2700 0.7429 0.2700
> 441 442 89.9 0.2700 13.9652 0.2700
> 441 443 89.9 0.2700 10.3452 0.2700
> 442 443 89.8 0.2700 4.5213 0.2700
> 544 545 90.1 0.2700 15.9781 0.2700
> 544 546 90.1 0.2700 30.0933 0.2700
> 545 546 90.1 0.2700 22.2106 0.2700
> 548 549 90.2 0.2700 25.9365 0.2700
> 548 550 90.7 0.2700 26.2207 0.2700
> 549 550 90.3 0.2700 14.0951 0.2700
> 549 551 91.6 0.2700 11.6914 0.2700
> 550 551 90.3 0.2700 21.9519 0.2700
> 553 554 90.7 0.2700 3.3299 0.2700
> 553 555 90.6 0.2700 3.9172 0.2700
> 554 555 92.9 0.2700 0.8229 0.2700
> 585 586 90.2 0.2700 11.2296 0.2700
> 585 587 90.3 0.2700 5.7745 0.2700
> 586 587 90.3 0.2700 7.9541 0.2700
> 610 611 90.3 0.2700 9.4740 0.2700
> 610 612 90.3 0.2700 8.4819 0.2700
> 611 612 90.3 0.2700 11.3421 0.2700
> 627 628 90.3 0.2700 8.1411 0.2700
> 627 629 90.4 0.2700 6.7729 0.2700
> 628 629 90.2 0.2700 13.2208 0.2700
> 658 659 90.2 0.2700 8.6001 0.2700
> 658 660 90.6 0.2700 3.1046 0.2700
> 659 660 90.3 0.2700 7.0261 0.2700
> 662 663 91.0 0.2700 2.3870 0.2700
> 662 664 90.9 0.2700 2.7549 0.2700
> 663 664 93.7 0.2700 0.6352 0.2700
> 679 680 90.3 0.2700 13.4498 0.2700
> 679 681 91.1 0.2700 16.7951 0.2700
> 680 681 90.4 0.2700 14.8215 0.2700
> 680 682 91.5 0.2700 13.3099 0.2700
> 681 682 90.3 0.2700 12.9139 0.2700
> 686 687 90.3 0.2700 9.1711 0.2700
> 686 688 90.1 0.2700 21.0202 0.2700
> 687 688 90.2 0.2700 15.7967 0.2700
> 692 693 90.3 0.2700 9.1086 0.2700
> 692 694 90.1 0.2700 26.5014 0.2700
> 693 694 90.1 0.2700 28.4044 0.2700
> 732 733 90.2 0.2700 8.9898 0.2700
> 732 734 90.1 0.2700 15.0593 0.2700
> 733 734 90.1 0.2700 19.4212 0.2700
> 765 766 90.2 0.2700 11.7151 0.2700
> 765 767 90.1 0.2700 17.2003 0.2700
> 766 767 90.3 0.2700 5.7251 0.2700
> 775 776 90.0 0.2700 23.4327 0.2700
> 775 777 90.0 0.2700 18.5738 0.2700
> 776 777 90.0 0.2700 7.5046 0.2700
> 779 780 90.1 0.2700 16.1949 0.2700
> 779 781 90.2 0.2700 4.8202 0.2700
> 780 781 90.1 0.2700 11.4123 0.2700
> 799 800 89.7 0.2700 27.3454 0.2700
> 799 801 89.6 0.2700 21.0301 0.2700
> 800 801 89.7 0.2700 13.7919 0.2700
> 800 802 89.3 0.2700 12.7552 0.2700
> 801 802 89.7 0.2700 26.5439 0.2700
> 832 833 89.5 0.2700 17.9044 0.2700
> 832 834 90.1 0.2700 20.5144 0.2700
> 833 834 89.9 0.2700 13.9714 0.2700
> 833 835 90.1 0.2700 17.8861 0.2700
> 834 835 89.6 0.2700 26.0753 0.2700
> 856 857 90.2 0.2700 10.1381 0.2700
> 856 858 90.2 0.2700 11.8072 0.2700
> 857 858 90.1 0.2700 16.2464 0.2700
> 885 886 90.1 0.2700 8.4484 0.2700
> 885 887 90.2 0.2700 4.0135 0.2700
> 886 887 90.2 0.2700 4.4632 0.2700
> 894 895 90.0 0.2700 14.5554 0.2700
> 894 896 90.0 0.2700 10.5658 0.2700
> 895 896 90.0 0.2700 13.5083 0.2700
> 902 903 90.2 0.2700 3.3980 0.2700
> 902 904 90.0 0.2700 17.1564 0.2700
> 903 904 90.0 0.2700 14.9801 0.2700
> 915 916 90.0 0.2700 17.1524 0.2700
> 915 917 90.0 0.2700 21.5888 0.2700
> 916 917 90.0 0.2700 5.2435 0.2700
> 941 942 90.0 0.2700 0.7282 0.2700
> 941 943 90.0 0.2700 0.7765 0.2700
> 942 943 90.0 0.2700 0.7311 0.2700
> 957 958 89.9 0.2700 15.0232 0.2700
> 957 959 90.0 0.2700 26.1044 0.2700
> 958 959 90.0 0.2700 25.6456 0.2700
> 961 962 94.3 0.2700 9.2229 0.2700
> 961 963 93.3 0.2700 9.6838 0.2700
> 962 963 92.5 0.2700 8.9941 0.2700
> 962 964 97.3 0.2700 4.4124 0.2700
> 963 964 97.2 0.2700 5.5336 0.2700
> 996 997 35.8 0.2700 0.2724 0.2700
> 1027 1028 90.0 0.2700 7.7884 0.2700
> 1027 1029 90.0 0.2700 6.7579 0.2700
> 1028 1029 90.0 0.2700 7.7841 0.2700
> 1039 1040 66.2 0.2700 0.3580 0.2700
> 1039 1041 31.9 0.2700 0.2668 0.2700
> 1040 1041 39.6 0.2700 0.3169 0.2700
> 1040 1042 89.5 0.2700 0.3264 0.2700
> 1041 1042 45.4 0.2700 0.3012 0.2700
> 1044 1045 93.5 0.2700 13.2243 0.2700
> 1044 1046 93.3 0.2700 14.8205 0.2700
> 1045 1046 91.7 0.2700 13.0874 0.2700
> 1045 1047 95.9 0.2700 8.3207 0.2700
> 1046 1047 93.9 0.2700 11.8244 0.2700
> 1065 1066 38.7 0.2700 0.2739 0.2700
> 1065 1067 60.8 0.2700 0.2732 0.2700
> 1074 1075 90.1 0.2700 0.4393 0.2700
> 1074 1076 64.3 0.2700 0.2699 0.2700
> 1075 1076 90.1 0.2700 0.3526 0.2700
> 1086 1087 90.2 0.2700 0.4147 0.2700
> 1086 1088 67.1 0.2700 0.3393 0.2700
> 1087 1088 90.2 0.2700 0.7327 0.2700
> 1087 1089 90.2 0.2700 0.7690 0.2700
> 1088 1089 90.1 0.2700 0.7878 0.2700
> 1118 1119 90.0 0.2700 0.9195 0.2700
> 1118 1120 38.5 0.2700 0.2696 0.2700
> 1119 1120 90.0 0.2700 0.9050 0.2700
> 1136 1137 62.3 0.2700 0.2896 0.2700
> 1137 1138 36.4 0.2700 0.2924 0.2700
> 1137 1139 44.8 0.2700 0.2942 0.2700
> 1141 1142 90.0 0.2700 11.4892 0.2700
> 1141 1143 90.0 0.2700 11.4891 0.2700
> 1142 1143 90.0 0.2700 11.4892 0.2700
> 3 4 90.0 0.2650 83.6337 0.2650
> 54 55 90.0 0.2600 23.8534 0.2600
> 60 61 90.0 0.2600 0.8260 0.2600
> 71 72 90.0 0.3100 27.7548 0.3100
> 109 110 90.0 0.3100 21.8345 0.3100
> 114 115 90.0 0.3100 0.8140 0.3100
> 116 117 90.0 0.3100 1.4351 0.3100
> 155 156 90.0 0.2600 4.3213 0.2600
> 173 174 90.0 0.2600 15.3048 0.2600
> 192 193 90.0 0.2600 0.3646 0.2600
> 203 204 90.0 0.2650 21.3496 0.2650
> 237 238 90.0 0.2650 7.2122 0.2650
> 247 248 90.0 0.2600 0.3020 0.2600
> 253 254 90.0 0.2600 0.3692 0.2600
> 255 256 90.0 0.2650 2.3883 0.2650
> 265 266 90.0 0.2600 0.2947 0.2600
> 275 276 90.0 0.2650 2.7267 0.2650
> 295 296 90.0 0.2600 34.2205 0.2600
> 303 304 90.0 0.2650 2.3091 0.2650
> 305 306 90.0 0.2600 47.5697 0.2600
> 314 315 90.0 0.2650 2.4219 0.2650
> 334 335 90.0 0.2650 33.8116 0.2650
> 336 337 90.0 0.2600 18.5406 0.2600
> 338 339 90.0 0.2650 17.4524 0.2650
> 340 341 90.0 0.2600 17.6973 0.2600
> 361 362 90.0 0.2650 13.8628 0.2650
> 367 368 90.0 0.2600 14.8104 0.2600
> 376 377 90.0 0.2650 7.2635 0.2650
> 392 393 90.0 0.2600 2.4593 0.2600
> 402 403 90.0 0.2650 1.7343 0.2650
> 404 405 90.0 0.2600 0.3920 0.2600
> 429 430 90.0 0.2650 0.5364 0.2650
> 437 438 90.0 0.2650 21.9520 0.2650
> 451 452 90.0 0.2600 1.4554 0.2600
> 468 469 59.7 0.2650 0.2650 0.2650
> 479 480 90.0 0.3100 18.8023 0.3100
> 485 486 90.0 0.2600 13.6847 0.2600
> 494 495 90.0 0.3100 7.7065 0.3100
> 500 501 90.0 0.2650 21.6147 0.2650
> 512 513 90.0 0.2650 17.9209 0.2650
> 534 535 83.6 0.3100 0.3100 0.3100
> 537 538 90.0 0.2600 4.4189 0.2600
> 541 542 90.0 0.3100 3.5603 0.3100
> 563 564 90.0 0.2600 31.5551 0.2600
> 579 580 90.0 0.3100 2.3912 0.3100
> 595 596 90.0 0.3100 4.4694 0.3100
> 600 601 90.0 0.3100 11.0915 0.3100
> 622 623 90.0 0.2600 12.0944 0.2600
> 636 637 90.0 0.3100 0.3940 0.3100
> 642 643 90.0 0.2650 14.4601 0.2650
> 652 653 90.0 0.3100 0.5690 0.3100
> 689 690 90.0 0.2600 6.6641 0.2600
> 699 700 90.0 0.2600 2.0476 0.2600
> 723 724 90.0 0.2600 20.7928 0.2600
> 725 726 90.0 0.2650 12.7657 0.2650
> 729 730 90.0 0.3100 0.9696 0.3100
> 749 750 90.0 0.2600 31.1056 0.2600
> 758 759 90.0 0.2650 21.0433 0.2650
> 760 761 90.0 0.2650 19.7754 0.2650
> 789 790 90.0 0.3100 0.7369 0.3100
> 793 794 90.0 0.2650 18.9454 0.2650
> 806 807 90.0 0.3100 1.9967 0.3100
> 823 824 90.0 0.2650 1.6391 0.2650
> 836 837 90.0 0.2600 0.6547 0.2600
> 853 854 90.0 0.2600 18.6495 0.2600
> 867 868 90.0 0.2600 17.8526 0.2600
> 871 872 90.0 0.2600 16.3901 0.2600
> 875 876 90.0 0.2600 17.4624 0.2600
> 905 906 90.0 0.2600 25.7169 0.2600
> 912 913 90.0 0.2600 14.7408 0.2600
> 921 922 90.0 0.2600 1.6534 0.2600
> 925 926 90.0 0.2600 33.0797 0.2600
> 931 932 90.0 0.3100 36.2703 0.3100
> 933 934 90.0 0.2650 51.8164 0.2650
> 1002 1003 90.0 0.2650 23.1537 0.2650
> 1050 1051 90.0 0.2650 18.2299 0.2650
> 1057 1058 90.0 0.2600 13.3863 0.2600
> 1059 1060 90.0 0.2600 24.0983 0.2600
> 1079 1080 90.0 0.2650 2.4137 0.2650
> 1081 1082 56.2 0.2600 0.2600 0.2600
> 1096 1097 90.0 0.2650 0.3483 0.2650
> 1099 1100 90.0 0.2650 12.3598 0.2650
> 1101 1102 90.0 0.2650 5.1454 0.2650
> 1111 1112 90.0 0.3100 0.3131 0.3100
> 1124 1125 46.8 0.2650 0.2650 0.2650
> 1133 1134 90.0 0.2600 3.6020 0.2600
> 1144 1145 90.0 0.2650 13.1949 0.2650
> Wrote pdb files with previous and current coordinates
> Segmentation fault
>
> Thanks,
>
> Sunny
>
>
> ------------------------------------------------------------------------
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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