AMBER Archive (2004)

Subject: AMBER: equilibration does not start with SHAKE

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Fri Apr 09 2004 - 17:30:55 CDT

Dear All,

I am having trouble with getting an equilibration startet when I try to
use SHAKE. The same system equilibrates nicely WITHOUT SHAKE! Therefore
I assume this is not the classical blowup problem described in the AMBER
FAQ's?
Also, it was possible to get the simulation started when I set the "tol"
parameter of shake to 0.0005, which is probably not acceptable?

I am using AMBER8 with the ff03 parameters, periodic boundary conditions
and a truncated octahedral TIP3P water box.

More specific information can be found below...

Any hints on what I might try are very much appreciated!

Thanks,
Oliver

------------

More information:

The system was thoroughly minimized.
The mdout file resulting from the first attempt to equilibrate the
minimized system looks like this:

NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 14.38 PRESS = 0.0
Etot = -203074.8675 EKtot= 1500.4620 EPtot = -204575.3295
BOND = 261.8307 ANGLE = 1243.2682 DIHED = 5032.7823
1-4 NB = 1748.9124 1-4 EEL = 21845.6532 VDWAALS = 28523.1903
EELEC =-263230.9666 EHBOND = 0.0000 RESTRAINT = 0.0000
  Ewald error estimate: 0.7828E-04
  --------------------------------------------------------------

      Coordinate resetting (SHAKE) was not accomplished
      within 3000 iterations

This is the corresponding md-input file:

---------------------------------------------------
md, nvt, warm to 298K slowly with restraint solute
  &cntrl
   imin = 0, irest = 0, ntx = 1,
   nstlim =20000, nsnb = 20, dt = .002,
   ntpr=100, ntwx=1000,
   ntt = 1, tempi=10.0, temp0 = 298.0, tautp=1,
   ntc = 2, ntf = 2,
   cut = 8., scee = 1.2,
   ntb = 1,
   ntr=1,
  &end
restrain the solute molecules
5.0
RES 1 532
END
END
----------------------------------------------------- 

-- 
_______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke_at_u.washington.edu
_______________________________________________________________

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