[gmx-users] Error during mdrun

[chetana baliga]

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?

Thanks,

Chetana.




> 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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