[gmx-users] core-dumped
Vytautas Rakeviius
vytautas1987 at yahoo.com
Wed Sep 12 11:55:52 CEST 2018
Investigate atoms 18720 and 18723 mentioned in error. From my experience such error happens when two atoms collide in completely unrealistic fashion.This error also dumps some pdb files at exact moment when things went really wrong and that ones you should look at.
Also I do not know what kind of settings file you used for minimization, but this one is my favorite: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp
You should try it.
On Tuesday, September 11, 2018, 7:33:25 AM GMT+3, Bratin Kumar Das <177cy500.bratin at nitk.edu.in> wrote:
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
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