On 7/14/15 3:07 AM, Sun Iba wrote:
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*
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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