[gmx-users] Error during mdrun
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
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,
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,
> 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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