Hello,
The linmin failures on the minimization are caused by the fact that the
minimizer can't find a minimum (and the direction it is looking in is
actually pointing uphill). However, if you're planning to run dynamics, the
principle role played by the minimization is to eliminate bad contacts so
that heating and equilibration can occur without a hitch (i.e. running into
numerous vlimit exceeded errors and having your initial dynamics die in a
heap of complaints).
In light of this I would suggest perhaps doing fewer steps with conjugate
gradient (increase ncyc to ~1000 perhaps). This will force 1000 steps of
steepest descent before switching to conjugate gradient. While using
steepest descent converges to the minimum far more slowly, it will quickly
get rid of highly unfavorable contacts (and that's what you're going for
anyway, right?). For dynamics you simply need to make sure that you're
starting from a reasonably representative structure, which this should
provide.
Also keep in mind that for an explicitly solvated system, a minimization
will likely play around with the waters more than it will with the protein
itself (unless the starting structure of the protein is VERY unfavorable).
Good luck!
Jason
On Tue, Oct 20, 2009 at 1:41 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber users,
>
> I am doing a simulation of a protein ligand complex.
>
> I get the the following error and the simulation stops during the
> production run:
>
> ----------------------------------------------------------
> Running from 0170 to 0180 at Tue Oct 20 19:21:39 IST 2009
> ----------------------------------------------------------
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 4580 9158 9159
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> rank 2 in job 15 compute-0-27.local_33789 caused collective abort of all
> ranks
> exit status of rank 2: killed by signal 9
>
> I have checked for this error message in the mailing list. The options to
> solve
> are increasing the size of the box (I increase from 10 to 14 angstroms)
> which in
> my case causes a linmin failure in the minimization step itself. I have
> checked
> the structure and could not find anything unusual.
> I do 2000 steps of minimization followed by 30ps of equillibration before
> the
> production run.
> I am attaching my minimization, equillibration and md scripts as follows:
>
>
> Minimization:
>
> # 2000 steps of minimization, no distance-dependent dielectric constant
> &cntrl
> maxcyc=2000, ncyc=100, imin=1, cut=10.0, igb=0, ntb=1, ntpr=1,
> lastist=8000000,
> &end
>
> Equillibration:
>
> Restraint improvement attempt
> &cntrl
> imin=0,
> ntr=1,
> ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
> ntf=2, ntb=1, igb=0, scnb=2.0, scee=1.2,
> cut=10.0,
> nstlim=5000, dt=0.002,
> tempi=0., temp0=300., ntt=1, tautp=0.5, dtemp=5.0,
> ntp=0, taup=0.5,
> ntc=2, tol=0.0001,
> vlimit=15,
> &end
> &ewald
> vdwmeth=1,
> &end
> Group for restrained atom
> 10.0
> RES 1 560
> END
> END
>
>
> MD:
>
> Equlibriation
> &cntrl
> imin=0,
> ntx=7, irest=1,
> ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
> ntf=2, ntb=2, igb=0, scnb=2.0, scee=1.2,
> cut=10.0,
> nscm=50,
> nstlim=5000, dt=0.002,
> tempi=300., temp0=300., ntt=1, tautp=0.5, dtemp=0.,
> ntp=1, taup=0.5,
> ntc=2, tol=0.00001,
> &end
> &ewald
> vdwmeth=1,
> &end
>
> I am also attaching the pdb file of my interest.
>
> I would be grateful if you please suggest me a way out of this problem.
> Thanks a lot in advance.
>
> Sincere Regards,
> Moitrayee Bhattacharyya
> Molecular Biophysics Unit
> Indian Institute of Science
> Bangalore - 560012
> India
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Oct 20 2009 - 20:30:03 PDT
