[gmx-users] LINCS WARNING
Justin Lemkul
jalemkul at vt.edu
Tue Jul 14 13:40:05 CEST 2015
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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