Dear all, During nvt equilibration I am getting the following error gmx mdrun -v -s npt.tpr -deffnm npt :-) GROMACS - gmx mdrun, 2016.5 (-:
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GROMACS: gmx mdrun, version 2016.5 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/workstation/Documents/GROMACS_projects/GROMACS_GCGR_GLUCAGON_2 Command line: gmx mdrun -v -s npt.tpr -deffnm npt Running on 1 node with total 4 cores, 4 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 Hardware topology: Basic Reading file npt.tpr, VERSION 2016.5 (single precision) Changing nstlist from 5 to 25, rlist from 1.2 to 1.233 Using 1 MPI thread Using 4 OpenMP threads WARNING: This run will generate roughly 6779 Mb of data starting mdrun '5YQZ_preprocessed - hbond-opt in water' 200000 steps, 400.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 7.344571, max 575.613892 (between atoms 18720 and 18723) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2379 2380 37.5 0.0872 0.1066 0.1010 2381 2382 47.9 0.1498 0.1052 0.1090 2383 2384 47.4 0.0884 0.1147 0.1090 2389 2390 49.1 0.0597 0.1001 0.0960 2426 2427 90.0 0.1253 0.1266 0.1080 4036 4037 54.9 0.1454 0.1077 0.1090 4038 4039 46.1 0.1081 0.1121 0.1090 4040 4041 30.2 0.0554 0.1124 0.1090 4040 4042 32.8 0.1002 0.1123 0.1090 4040 4043 35.1 0.1426 0.1129 0.1090 5382 5384 50.3 0.1280 0.1093 0.1090 5956 5957 37.0 0.0770 0.1141 0.1090 5956 5959 89.8 0.1805 0.1828 0.1090 5960 5961 61.7 0.1651 0.1267 0.1229 6029 6031 89.9 0.1146 1.2008 0.1090 6035 6036 31.6 0.1083 0.1036 0.1010 6038 6040 42.5 0.1324 0.1043 0.1010 6887 6888 31.1 0.1070 0.1111 0.1090 6887 6889 59.5 0.1351 0.1100 0.1090 13006 13007 42.3 0.1575 0.1385 0.1610 13007 13008 41.7 0.1436 0.1329 0.1480 13007 13009 90.0 0.1348 0.2201 0.1480 13007 13010 38.2 0.1530 0.1563 0.1610 18672 18673 86.0 0.1515 0.2646 0.1530 18673 18674 92.0 0.1407 1.1474 0.1430 18674 18675 124.6 0.1445 23.3042 0.1610 18675 18677 82.6 0.1723 23.9350 0.1480 18675 18678 106.9 0.1522 23.6614 0.1610 18678 18679 89.6 0.1402 0.9389 0.1430 18679 18680 92.0 0.1552 0.1875 0.1530 18723 18724 62.7 0.1687 73.2199 0.1470 18724 18725 89.5 0.1607 0.8262 0.1530 18725 18726 90.8 0.1420 0.1872 0.1430 18720 18723 156.7 0.1620 84.7622 0.1470 18721 18723 66.7 0.1602 72.9378 0.1470 18722 18723 67.9 0.1335 72.8562 0.1470 20543 20544 88.9 0.1496 0.1505 0.1470 20544 20545 30.8 0.1570 0.1781 0.1530 20540 20543 89.5 0.1331 0.2780 0.1470 20541 20543 89.3 0.1499 0.1735 0.1470 20542 20543 89.2 0.1426 0.1755 0.1470 Wrote pdb files with previous and current coordinates step 0 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.060079, max 4.753909 (between atoms 18723 and 18724) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2381 2382 91.7 0.1052 0.1585 0.1090 2426 2427 89.9 0.1266 0.1348 0.1080 3148 3163 63.4 0.1598 0.1607 0.1522 3163 3164 56.3 0.1267 0.1374 0.1229 4036 4037 61.4 0.1077 0.1036 0.1090 5382 5384 57.9 0.1093 0.1084 0.1090 5956 5959 89.7 0.1828 0.1869 0.1090 5960 5961 89.8 0.1267 0.1713 0.1229 6029 6031 88.4 1.2008 0.1217 0.1090 6038 6040 42.5 0.1043 0.0979 0.1010 6887 6889 89.8 0.1100 0.1079 0.1090 13006 13007 39.8 0.1385 0.1539 0.1610 13007 13008 34.7 0.1329 0.1585 0.1480 13007 13009 90.1 0.2201 0.1396 0.1480 13007 13010 34.8 0.1563 0.1584 0.1610 18672 18673 90.6 0.2646 0.1529 0.1530 18673 18674 91.7 1.1474 0.1412 0.1430 18674 18675 83.9 23.3042 0.1117 0.1610 18675 18677 83.9 23.9350 0.1883 0.1480 18675 18678 76.6 23.6614 0.1548 0.1610 18678 18679 90.3 0.9389 0.1455 0.1430 18679 18680 90.7 0.1875 0.1534 0.1530 18723 18724 67.7 73.2199 0.8458 0.1470 18724 18725 89.8 0.8262 0.8169 0.1530 18725 18726 89.9 0.1872 0.5024 0.1430 18720 18723 43.1 84.7622 0.4501 0.1470 18721 18723 67.4 72.9378 0.6694 0.1470 18722 18723 70.6 72.8562 0.6095 0.1470 20543 20544 92.0 0.1505 0.1906 0.1470 20544 20545 59.1 0.1781 0.1071 0.1530 20540 20543 89.3 0.2780 0.1317 0.1470 20541 20543 92.0 0.1735 0.1469 0.1470 20542 20543 92.0 0.1755 0.1421 0.1470 step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) My minimization ran properly. I can't understang why it is happening -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.