[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
Follow me on ResearchGate<https://www.researchgate.net/profile/Carlos_Almeciga-Diaz/>
Google Scholar<https://scholar.google.com.co/citations?hl=en&user=dk9mHOMAAAAJ>

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