On Fri, Apr 09, 2004, Oliver Hucke wrote:
>
> I am having trouble with getting an equilibration startet when I try to
> use SHAKE. The same system equilibrates nicely WITHOUT SHAKE!
>
> The system was thoroughly minimized.
Did you minimize with or without SHAKE?
> 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
Suggestions:
(1) try a short run, with ntpr=1. This is always a good idea when you
have problems, as it tells you a lot more about what is going on.
(2) Use a shorter dt for equilibration, say 0.001 or even 0.0005.
(3) Initially heat to a lower temperature.
(4) Since the system seems to equilibrate OK without shake, take that
equlibrated restart file, and try to continue from that point, turning shake on.
....good luck...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Sat Apr 10 2004 - 00:53:00 PDT
