[gmx-users] Error during mdrun

chetana baliga baliga.chetana at gmail.com
Tue Jan 9 15:41:04 CET 2007

Thanks, Tsjerk and Mark.  Here's what the end of my log file says :

           Step           Time         Lambda
        5243900    10487.80078        0.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.019872     61     62   0.004609
        After LINCS         0.000051     35     37   0.000020

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    1.58108e+02    9.30052e+01    4.86079e+01    6.91807e+00    1.08849e+03
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
    3.04429e+04   -1.88462e+05   -1.73048e+04   -1.73929e+05    3.14049e+04
   Total Energy    Temperature Pressure (bar)
   -1.42524e+05    3.00225e+02    3.27136e+01

t = 10487.916 ps: Water molecule starting at atom 6211 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Large VCM(group rest):   -440.66449,      0.00000,   -110.16612,
ekin-cm:  7.85519e+09

My peptide is a decapeptide, and yes, it does contain a lysine, but
the error doesnt involve its atoms.  I am running my simualtions under
npt conditions. I initially did a pr run of a total of 600 ps, initial
200ps being under nvt conditions and the remaining under npt [as
suggested in the archives, that initial nvt run helps the system to
relax] After the pr, the system had equilibrated quite well, though
the pressure average was 5.85 bar , while the ref_p was 1 bar. The
solvent used is SPC water, and the coulomb type is PME.

And, there were no other LINCS warnings in the md0.log file.

 Could you please advise me on this?



> Hi Chetana (and Mark et al.),
> Note that this can also be the infamous spinning -NH3 error, which has
> been reported primarily for lysines previously on this list (tip:
> search the archive). To be sure, as Mark stated, more information is
> required. Specifically, at what step the crash occurred and which
> atoms were involved. This information is given in the *0.log file.
> Although the crash will be at the end of the file, the problem may
> have gone on for some while and you will have to search for the first
> hint of problems (LINCS warning), and check the atoms involved.
> If the crash occurs early during your simulation, it is likely a
> problem of equilibration/setup.
> (Now why am I always lagging behind Mark with my comments?)...
> Hope it helps,
> Tsjerk
> On 1/9/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > > Dear all,
> > > At times during the md run of my peptide, the run crashes and I get the
> > > following error displayed -
> > >
> > > "Wrote pdb files with previous and current coordinates
> > > Wrote pdb files with previous and current coordinates
> > > MPI process rank 0 (n0, p3089) caught a SIGSEGV.
> > > MPI process rank 1 (n0, p3090) caught a SIGSEGV."
> >
> > We'll need more information from the output to be sure, but I suspect if
> > you look just before this part of the logfile, you'll see LINCS errors,
> > indicating you probably haven't minimized or equilibrated well enough.
> >
> > Mark
> >
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