[gmx-users] Error during mdrun
Mark.Abraham at anu.edu.au
Wed Jan 10 06:09:24 CET 2007
chetana baliga wrote:
> 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?
OK, the water "can not be settled" is a reference to SETTLE, which is a
constraint-enforcing algorithm for water... so we were on the right
track with the suspicion of LINCS errors (another such algorithm).
This time step is quite a long time away from your equilibration time
(assuming you set t=0 at the start of equilibration) for such an error
to arise. I would first have a look at your trajectory just before that
time and see if you can deduce anything from the behaviour, especially
of and near atom 6211.
Over what length of time did you observe the average pressure of 5.85
bar? You shouldn't be including the initial period, since it almost
certainly was very large then, and will be throwing off your statistics.
If you have xmgrace installed, use g_energy -W to look at a graphical
plot of pressure with time in the both the NPT equilibration and the NPT
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