[gmx-users] mdrun segmentation fault

[Erik Lindahl]

Hi,

Have a look at the coordinates in the PDB file that mdrun is dumping.
You will likely see that a group of atoms (e.g. a sidechain) is
moving violently and/or breaking up completely just before the crash.

There can be plenty of reasons for this. One possibility is that you
have a small number of Na ions that you temperature-couple
separately. If one of the is bumping into or interacting with e.g. a
particular sidechain this can lead to very large velocity scaling.

Cheers,

Erik


On Jun 26, 2006, at 5:59 PM, Jim Fonseca wrote:

> Hi,
> 	I'm having a problem with mdrun seg-faulting after ~240 ps of  
> unrestrained simulation.  I'm using 3.3.1 on a beowulf cluster.   
> Below are the tails of the output files.  I've also listed the .mdp  
> at the end.
>
> I've tried varying some of the parameters(dt and tau_p), but the  
> simulations always seem to run to about 200 ps before crashing.   
> How can I find out more information about what's going on here?   
> The EM (run to machine convergence) and PR (100 ps) always run  
> fine.  It seems to me that if it was an equilibration problem, it'd  
> happen before running for so long.
>
>
> Thanks for any help!
> Jim Fonseca
>
>
>
> *log from parallel node 0*
>            Step           Time         Lambda
>          120000      240.00000        0.00000
>
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.067432   7188   7189   0.005393
>         After LINCS         0.000131   8250   8253   0.000021
>
>    Energies (kJ/mol)
>           Angle    Proper Dih. Ryckaert-Bell.  Improper  
> Dih.          LJ-14
>     7.02762e+04    2.34867e+04    2.53603e+04    7.54128e+03     
> 2.46027e+04
>      Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.       
> Potential
>     1.54268e+05    2.16502e+05   -2.96632e+06   -6.02749e+05    
> -3.04703e+06
>     Kinetic En.   Total Energy    Temperature Pressure (bar)
>     5.09231e+05   -2.53780e+06    2.99996e+02    3.08941e+01
>
> *output redirect fom mdrun*
> ^Mstep 120180, will finish at Wed Jun 28 13:04:09 2006
> ^Mstep 120190, will finish at Wed Jun 28 13:04:13 2006
> ^Mstep 120200, will finish at Wed Jun 28 13:04:17 2006
>
> Back Off! I just backed up step120205.pdb to ./#step120205.pdb.1#
>
> Back Off! I just backed up step120206.pdb to ./#step120206.pdb.1#
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> Back Off! I just backed up step120206.pdb to ./#step120206.pdb.2#
>
> Back Off! I just backed up step120206.pdb to ./#step120206.pdb.3#
>
> Back Off! I just backed up step120207.pdb to ./#step120207.pdb.1#
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> Back Off! I just backed up step120207.pdb to ./#step120207.pdb.2#
>
> Back Off! I just backed up step120207.pdb to ./#step120207.pdb.3#
>
> Back Off! I just backed up step120207.pdb to ./#step120207.pdb.4#
>
> Back Off! I just backed up step120208.pdb to ./#step120208.pdb.1#
>
> Back Off! I just backed up step120208.pdb to ./#step120208.pdb.2#
>
> Back Off! I just backed up step120208.pdb to ./#step120208.pdb.3#
> 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
> mpiexec: Warning: tasks 7-13 died with signal 11 (Segmentation fault).
>
>
>
> *full.mdp*
> title                    = 2agv_full
> cpp                      = /usr/bin/cpp
> ;include                  = -I../top
> ;define                   = -DPROPOSRES -DLIPPOSRES
> constraints              = all-bonds
> integrator               = md
> tinit                    = 0.0
> dt                       = 0.002
> nsteps                   = 500000   ;1000 ps
> nstxout                  = 10000
> nstvout                  = 10000
> nstlog                   = 10000
> nstenergy                = 1000
> nstxtcout                = 1000
> xtc_grps                 = Protein  SOL POP Na
> energygrps               = Protein  SOL POP Na
> nstlist                  = 10
> ns_type                  = grid
> rlist                    = 1.4
> coulombtype              = PME
> rcoulomb                 = 1.4
> rvdw                     = 1.4
> tcoupl                   = Berendsen
> tc-grps                  = Protein      SOL    POP Na
> tau_t                    = 0.1  0.1  0.1 0.1
> ref_t                    = 300  300  300 300
> Pcoupl                   = Berendsen
> pcoupltype               = anisotropic
> tau_p                    = 1.00
> compressibility          = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
> ref_p                    = 1.0 1.0 1.0 0.0 0.0 0.0
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = -1
> optimize_fft             = yes
>
>
>
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