[gmx-users] Segmentation fault in mdrun nvt
Smith, Micholas D.
smithmd at ornl.gov
Wed Apr 8 19:59:30 CEST 2015
Could you put up what your run parameters were (you .mdp file for the simulation)? It is nearly impossible to determine the problem without it.
-Micholas
===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Carlos Javier Almeciga Diaz <cjalmeciga at javeriana.edu.co>
Sent: Wednesday, April 08, 2015 1:56 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Segmentation fault in mdrun nvt
Dear all,
I'm running a simulation by using Gromacs 4.5.5. Everything was going well. For instance, energy minimization results were:
Potential Energy = -2.506 e+06
Maximum force = 9.116 e+02 on atom 9465
Norm of force = 1.588 e+01
However, when I run /mdrun -deffnm nvt, I got Segmentation fault after the first step:
---
Back Off! I just backed up nvt.log to ./#nvt.log.2#
Reading file nvt.tpr, VERSION 4.5.5 (single precision)
Starting 8 threads
Making 1D domain decomposition 8 x 1 x 1
Back Off! I just backed up nvt.trr to ./#nvt.trr.2#
Back Off! I just backed up nvt.edr to ./#nvt.edr.2#
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002769, max 0.066914 (between atoms 9467 and 9466)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
starting mdrun 'Protein in water'
50000 steps, 100.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 551.695682, max 16612.693359 (between atoms 9469 and 9468)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
9449 9474 33.3 0.1525 0.2026 0.1520
9474 9475 34.4 0.1533 0.1972 0.1530
9474 9473 126.6 0.1444 2.5436 0.1440
9450 9449 36.2 0.1525 0.2098 0.1520
9453 9450 117.4 0.1524 2.4581 0.1520
9451 9450 36.9 0.1442 0.1934 0.1440
9456 9453 134.1 0.1530 6.3248 0.1520
9454 9453 103.2 0.1443 2.4653 0.1440
9455 9454 45.6 0.1000 0.1465 0.1000
6749 6751 54.5 0.1473 27.5262 0.1470
6749 6750 64.3 0.1002 27.3363 0.1000
6747 6749 71.6 0.1338 58.5743 0.1330
6747 6748 87.1 0.1236 66.7860 0.1230
6739 6747 61.8 0.1544 423.3893 0.1530
6739 6740 89.5 0.1564 305.2773 0.1530
6740 6741 52.5 0.1544 837.0554 0.1530
6741 6743 90.0 0.1347 2499.9929 0.1330
6741 6742 90.5 0.1337 1221.3651 0.1330
6737 6739 67.7 0.1481 420.8361 0.1470
6737 6738 72.1 0.1003 64.4424 0.1000
6735 6737 75.8 0.1334 72.8422 0.1330
6735 6736 61.5 0.1232 20.9598 0.1230
6728 6735 53.8 0.1532 21.0112 0.1530
6758 6760 36.4 0.1331 0.1849 0.1330
6758 6759 37.2 0.1231 0.1704 0.1230
9456 9473 57.7 0.1451 9.3411 0.1440
9457 9456 73.4 0.1462 13.9615 0.1440
9458 9457 99.7 0.1491 73.1622 0.1440
9469 9458 72.0 0.1576 304.7723 0.1520
9459 9458 82.4 0.1569 98.6739 0.1520
9462 9459 89.1 0.1563 191.2612 0.1520
9460 9459 81.3 0.1472 70.0695 0.1440
9461 9460 89.0 0.1010 1.3343 0.1000
9465 9462 79.6 0.1519 1302.8002 0.1520
9463 9462 100.7 0.1478 182.7150 0.1440
9464 9463 59.2 0.1013 91.4692 0.1000
9468 9465 100.5 0.1487 1679.1453 0.1440
9466 9465 66.2 0.1496 1021.5928 0.1440
9467 9466 94.6 0.1067 466.8471 0.1000
9469 9468 79.1 0.1466 2392.3718 0.1440
9469 9470 154.4 0.1578 216.1825 0.1530
9470 9471 33.9 0.1447 113.4756 0.1430
9471 9472 94.3 0.1002 59.3628 0.1000
6751 6758 115.9 0.1532 0.3530 0.1530
6751 6752 116.6 0.1531 0.3475 0.1530
6752 6753 37.6 0.1531 0.2066 0.1530
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 574.353441, max 22322.214844 (between atoms 6743 and 6745)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
6741 6743 90.0 0.1347 2499.9524 0.1330
6741 6742 90.5 0.1337 1221.2900 0.1330
6742 6744 79.6 0.1331 227.1442 0.1330
6743 6745 87.7 0.1348 2968.9878 0.1330
6744 6745 90.9 0.1330 176.8934 0.1330
6745 6746 92.8 0.1001 129.7189 0.1000
6724 6726 35.7 0.1330 0.1739 0.1330
6726 6728 113.1 0.1470 0.2366 0.1470
6726 6727 39.2 0.1000 0.1362 0.1000
6728 6735 54.0 0.1532 21.1253 0.1530
6728 6729 118.6 0.1530 0.2115 0.1530
6729 6730 36.6 0.1530 0.1977 0.1530
6735 6737 75.8 0.1334 72.8788 0.1330
6735 6736 61.4 0.1232 20.9331 0.1230
6737 6739 67.7 0.1481 420.8405 0.1470
6737 6738 72.1 0.1003 64.4355 0.1000
6739 6747 61.8 0.1544 423.3926 0.1530
6739 6740 89.5 0.1564 305.2860 0.1530
6740 6741 52.5 0.1544 837.0526 0.1530
6747 6749 71.6 0.1338 58.5763 0.1330
6749 6751 54.5 0.1473 27.5262 0.1470
6751 6758 115.9 0.1532 0.3530 0.1530
6758 6760 36.3 0.1331 0.1845 0.1330
6758 6759 37.2 0.1231 0.1704 0.1230
6751 6752 116.6 0.1531 0.3475 0.1530
6752 6753 37.6 0.1531 0.2066 0.1530
6749 6750 64.3 0.1002 27.3363 0.1000
6747 6748 87.1 0.1236 66.7878 0.1230
9471 9470 33.9 0.1447 113.4756 0.1430
9469 9470 154.4 0.1578 216.1825 0.1530
9469 9468 79.1 0.1466 2392.3718 0.1440
9465 9468 100.5 0.1487 1679.1451 0.1440
9465 9466 66.2 0.1496 1021.5931 0.1440
9466 9467 94.6 0.1067 466.8471 0.1000
9462 9465 79.6 0.1519 1302.7970 0.1520
9462 9463 100.7 0.1478 182.7062 0.1440
9459 9462 89.1 0.1563 191.2630 0.1520
9458 9469 72.0 0.1576 304.7721 0.1520
9458 9459 82.4 0.1569 98.6732 0.1520
9459 9460 81.3 0.1472 70.0686 0.1440
9460 9461 89.0 0.1010 1.3341 0.1000
9458 9457 99.7 0.1491 73.1620 0.1440
9456 9457 73.4 0.1462 13.9615 0.1440
9453 9456 134.1 0.1530 6.3248 0.1520
9472 9471 94.3 0.1002 59.3628 0.1000
9474 9473 126.6 0.1444 2.5436 0.1440
9456 9473 57.7 0.1451 9.3411 0.1440
9453 9454 103.2 0.1443 2.4653 0.1440
9454 9455 45.6 0.1000 0.1465 0.1000
9450 9453 117.4 0.1524 2.4581 0.1520
9450 9451 36.9 0.1442 0.1934 0.1440
9449 9450 36.2 0.1525 0.2098 0.1520
9475 9474 34.4 0.1533 0.1972 0.1530
9449 9474 33.3 0.1525 0.2026 0.1520
Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2#
Back Off! I just backed up step0b_n4.pdb to ./#step0b_n4.pdb.2#
Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2#
Back Off! I just backed up step0c_n4.pdb to ./#step0c_n4.pdb.2#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault
---
Any idea where is the problem?
Regards,
Javier
---
Carlos Javier Alméciga Díaz, QF., Ph.D.
Profesor Asociado
Pontificia Universidad Javeriana
Facultad de Ciencias
Instituto de Errores Innatos del Metabolismo
Http://www.javeriana.edu.co/ieim<http://www.javeriana.edu.co/ieim>
Tel: +57-1-3208320 Ext 4140
Fax: +57-1-3208320 Ext 4099
Bogotá D.C. - Colombia
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Google Scholar<https://scholar.google.com.co/citations?hl=en&user=dk9mHOMAAAAJ>
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