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
Received on Tue Oct 20 2009 - 19:30:03 PDT
