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.u.washington.edu
_______________________________________________________________
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Received on Fri Apr 09 2004 - 23:53:00 PDT
