[gmx-users] Segmentation fault after mdrun for MD simulation

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 18 02:55:52 CEST 2011



rainy908 wrote:
> Dear gmx-users:
> 
> Thanks Justin for your help.  But now I am experiencing a Segmentation fault error when executing mdrun.  I've perused the archives but found none of the threads on segmentation faults similar to my case here.  I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%.  Any advice would be especially welcome.
> 
> My files are as follows:
> 
> md.mdp
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> title               = 1JFF MD
> cpp                 = /lib/cpp ; location of cpp on SGI
> constraints         = all-bonds
> integrator          = md
> dt                  = 0.0001 ; ps
> nsteps              = 25000 ;
> nstcomm             = 1
> nstxout             = 500 ; output coordinates every 1.0 ps
> nstvout             = 0
> nstfout             = 0
> nstlist             = 10
> ns_type             = grid
> rlist               = 0.9
> coulombtype         = PME
> rcoulomb            = 0.9
> rvdw                = 1.0
> fourierspacing      = 0.12
> fourier_nx        = 0
> fourier_ny        = 0
> fourier_nz        = 0
> pme_order         = 6
> ewald_rtol        = 1e-5
> optimize_fft      = yes
> ; Berendsen temperature coupling is on in four groups
> Tcoupl                = berendsen
> tau_t                 = 0.1
> tc-grps               = system
> ref_t                 = 310
> ; Pressure coupling is on
> Pcoupl              = berendsen
> pcoupltype          = isotropic
> tau_p               = 0.5
> compressibility     = 4.5e-5
> ref_p               = 1.0
> ; Generate velocites is on at 310 K.
> gen_vel             = yes
> gen_temp = 310.0
> gen_seed = 173529
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
> error output file:
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ..
> ..
> Back Off! I just backed up md.log to ./#md.log.1#
> Getting Loaded...
> Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision)
> Starting 8 threads
> Loaded with Money
>  
> Making 3D domain decomposition 2 x 2 x 2
>  
> Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1#
> 
> Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1#
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.046849, max 1.014038 (between atoms 8541 and 8539)
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.001453, max 0.034820 (between atoms 315 and 317)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> 

If mdrun is failing at step 0, it indicates that your system is physically 
unreasonable.  Either the starting configuration has atomic clashes that have 
not been resolved (and thus you need better EM and/or equilibration) or that the 
parameters assigned to the molecules in your system are unreasonable.

-Justin

> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.048739, max 1.100685 (between atoms 8422 and 8421)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> ..
> ..
> <snip>
> ..
> ..
> 
> starting mdrun 'TUBULIN ALPHA CHAIN'
> 25000 steps,     50.0 ps.
> Warning: 1-4 interaction between 8443 and 8446 at distance 2.853 which is larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size   
> ..
> ..
> <snip>
> ..
> ..
> step 0: Water molecule starting at atom 23781 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 
> Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1#
> 
> Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1#
> 
> Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2#
> 
> Back Off! I just backed up step0b_n3.pdb to ./#step0b_n3.pdb.2#
> 
> Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1#
> 
> Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1#
> 
> Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2#
> 
> Back Off! I just backed up step0c_n3.pdb to ./#step0c_n3.pdb.2#
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> ^Mstep 0/opt/sge/jacobson/spool/node-2-05/job_scripts/1097116: line 21:  1473 Segmentation fault      (core dumped) $MDRUN -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s 1JFF_md.tpr -o 1JFF_md.trr -c 1JFF_pmd.gro -x 1JFF_md.xtc -e 1JFF_md.edr
> 
> 
> 
> On 16 August 2011 10:58, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>     rainy908 wrote:
> 
>         Hi,
> 
>         I get the error "Atomtype CR1 not found" when I execute grompp.  After perusing the gmx archives, I understand this error has to do with the lack of "CR1" being specified in the force field.  However, I did include the appropriate .itp files in my .top file (shown below).  As you can see, obviously CR1 is specified in taxol.itp and gtp.itp.  Therefore, I'm not sure what exactly is the problem here.
> 
> 
>     You're mixing and matching force fields.  PRODRG produces Gromos-compatible parameters (and does a poor job of that - I can tell you now that the charges assigned to the aromatic C and H of taxol are total junk).  You're then trying to combine these parameters with OPLS.  Even if you could somehow hack the topology together, the results would be useless.
> 
>     For more about the hazards of PRODRG, see http://pubs.acs.org/doi/abs/10.1021/ci100335w.
> 
>     The solution is to pick a force field and apply it uniformly to the system you're working with.
> 
>     -Justin
> 
>         Any input on this issue would be greatly appreciated.
> 
>         1JFF.top
>         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>         ;       File '1JFF.top' was generated
>         ;       By user: onbekend (0)
>         ;       On host: onbekend
>         ;       At date: Mon Aug 15 17:22:01 2011
>         ;
>         ;       This is a standalone topology file
>         ;
>         ;       It was generated using program:
>         ;       pdb2gmx - VERSION 4.5.3
>         ;
>         ;       Command line was:
>         ;       /software/gromacs/gromacs-4.5.3-x86_64/bin/pdb2gmx -f 1JFF_new.pdb -o 1JFF.gro -p 1JFF.top
>         ;
>         ;       Force field was read from the standard Gromacs share directory.
>         ;
> 
>         ; Include forcefield parameters
>         #include "oplsaa.ff/forcefield.itp"
>         #include "taxol.itp"
>         #include "gdp.itp"
>         #include "gtp.itp"
> 
>         ; Include chain topologies
>         #include "1JFF_Protein_chain_A.itp"
>         #include "1JFF_Protein_chain_B.itp"
>         #include "1JFF_Ion_chain_A2.itp"
> 
>         ; Include water topology
>         #include "oplsaa.ff/spc.itp"
> 
>         #ifdef POSRES_WATER
>         ; Position restraint for each water oxygen
>         [ position_restraints ]
>         ;  i funct       fcx        fcy        fcz
>           1    1       1000       1000       1000
>         #endif
> 
>         ; Include topology for ions
>         #include "oplsaa.ff/ions.itp"
> 
>         [ system ]
>         ; Name
>         TUBULIN ALPHA CHAIN; TUBULIN BETA CHAIN in water
> 
>         [ molecules ]
>         ; Compound        #mols
>         Protein_chain_A     1
>         Protein_chain_B     1
>         Ion_chain_A2        1
>         Taxol               1
>         GDP                 1
>         GTP                 1
>         SOL             21016
>         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
>         taxol.itp
>         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>         ;       This file was generated by PRODRG version AA081006.0504
>         ;       PRODRG written/copyrighted by Daan van Aalten
>         ;       and Alexander Schuettelkopf
>         ;
>         ;       Questions/comments to dava at davapc1.bioch.dundee.ac.uk
>         ;
>         ;       When using this software in a publication, cite:
>         ;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
>         ;       PRODRG - a tool for high-throughput crystallography
>         ;       of protein-ligand complexes.
>         ;       Acta Crystallogr. D60, 1355--1363.
>         ;
>         ;
> 
>         [ moleculetype ]
>         ; Name nrexcl
>         TA1      3
> 
>         [ atoms ]
>         ;   nr      type  resnr resid  atom  cgnr   charge     mass
>             1       CR1     1  TA1     C05     1   -0.015  12.0110
>             2        HC     1  TA1     H05     1    0.015   1.0080
>             3       CR1     1  TA1     C06     2   -0.012  12.0110
>             4        HC     1  TA1     H06     2    0.019   1.0080
>             5       CR1     1  TA1     C07     2   -0.012  12.0110
>             6        HC     1  TA1     H07     2    0.019   1.0080
>             7       CR1     1  TA1     C08     2   -0.012  12.0110
>             8        HC     1  TA1     H08     2    0.019   1.0080
>             9       CR1     1  TA1     C09     2   -0.012  12.0110
>            10        HC     1  TA1     H09     2    0.019   1.0080
>            11         C     1  TA1     C04     2   -0.028  12.0110
>            12         C     1  TA1     C03     3    0.357  12.0110
>            13         O     1  TA1     O03     3   -0.710  15.9994
>            14        OA     1  TA1     O02     3   -0.186  15.9994
>            15       CH1     1  TA1     C02     3    0.235  13.0190
>            16       CH1     1  TA1     C10     3    0.148  13.0190
>            17       CH1     1  TA1     C11     3    0.156  12.0110
>            18        OA     1  TA1     O04     4   -0.175  15.9994
>            19         C     1  TA1     C12     4    0.378  12.0110
>            20         O     1  TA1     O05     4   -0.670  15.9994
>         ...
>         ...
>         <snip>
>         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
>         gtp.itp
>         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>         [ moleculetype ]
>         ; Name nrexcl
>         GTP      3
> 
>         [ atoms ]
>         ;   nr      type  resnr resid  atom  cgnr   charge     mass
>             1         O     1  GTP      O6     1   -0.266  15.9994
>             2         C     1  GTP      C6     1    0.216  12.0110
>             3        NR     1  GTP      N1     1   -0.008  14.0067
>             4         H     1  GTP      H1     1   -0.020   1.0080
>             5         C     1  GTP      C2     1    0.322  12.0110
>             6        NT     1  GTP      N2     1   -0.001  14.0067
>             7         H     1  GTP     H22     1   -0.020   1.0080
>             8         H     1  GTP     H21     1   -0.020   1.0080
>             9        NR     1  GTP      N3     1   -0.203  14.0067
>            10         C     1  GTP      C4     2    0.133  12.0110
>            11         C     1  GTP      C5     2    0.048  12.0110
>            12        NR     1  GTP      N7     2   -0.321  14.0067
>            13       CR1     1  GTP      C8     2   -0.037  12.0110
>            14        HC     1  GTP      H8     2   -0.019   1.0080
>            15        NR     1  GTP      N9     2    0.112  14.0067
>            16       CH1     1  GTP     CAU     2    0.084  13.0190
>         ..
>         ..
>         <snip>
>         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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