AMBER Archive (2009)

Subject: [AMBER] simulation blown up

Date: Tue Oct 20 2009 - 12:41:29 CDT

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:


# 2000 steps of minimization, no distance-dependent dielectric constant
 maxcyc=2000, ncyc=100, imin=1, cut=10.0, igb=0, ntb=1, ntpr=1,


Restraint improvement attempt
    ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
    ntf=2, ntb=1, igb=0, scnb=2.0, scee=1.2,
    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,
Group for restrained atom
RES 1 560


    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,
    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,

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

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