From your input, you are asking for temp0 to jump from 300 to 400
within the first 200 steps (seems short). But, you only show the output
for step=10. Can you tell us what happens by the time you get further
along ?
adrian
pascal.baillod.epfl.ch wrote:
> Dear Amber developers,
>
> I am trying to use Amber8 for a GB implicit solvent simulation with langevin
> dynamics (ntt=3) of a 12 bp rna tetraloop. I would like to use simulated
> annealing (SA), but whatever I do the temperature stays at 300.0. I read a
> message on the mailing list that says that SA is not possible with langevin
> dynamics. So I tried the same with the berendsen thermostat (ntt=1), but again,
> no change in temperature. With explicit solvent, however, it works. Dose that
> mean SA is not implemented for GB and/or langevin? You can find my input and
> ouput here below. The latter seems to confirm that the SA weight change input
> was read in..
>
> Thank you very much for your help!
>
> Pascal
>
>
> equilibr
> &cntrl
> IMIN = 0,
> NTX = 5,
> IREST = 1,
> NTPR = 10,
> NMROPT = 1,
> NTWR = 10000,
> NTWX = 500,
> NTF = 1,
> NTB = 0,
> DIELC = 1.0,
> CUT = 1000.0,
> SCNB = 2.0,
> SCEE = 1.2,
> NSTLIM = 2000000,
> NSCM = 1000,
> DT = 0.0015,
> NTT = 1,
> NTC = 2,
> TOL = 0.00001,
> NTR = 0,
> IBELLY = 0,
> IVCAP = 0,
> IGB = 1,
> VLIMIT=10,
> &end
> &ewald
> eedmeth=4,
> &end
> &wt
> TYPE='TEMP0', istep1=0, istep2=200, value1=300.0, value2=400.0,
> &end
> &wt
> TYPE='TEMP0', istep1=201, istep2=1000, value1=400.0, value2=400.0,
> &end
> &wt
> TYPE='END'
> &end
>
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> TEMP0 0 200 300.000000 400.000000 0 0
> TEMP0 201 1000 400.000000 400.000000 0 0
>
> RESTRAINTS:
> ** No restraint defined **
>
> Done reading weight changes/NMR restraints
>
>
> Number of triangulated 3-point waters found: 0
> | Atom division among processors:
> | 0 389
> | Running AMBER/MPI version on 1 nodes
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
> --------------------------------------------------------------------------------
>
>
> NSTEP = 10 TIME(PS) = 3000.015 TEMP(K) = 313.74 PRESS = 0.0
> Etot = -2193.2307 EKtot = 320.4587 EPtot = -2513.6894
> BOND = 109.3584 ANGLE = 235.9093 DIHED =
>
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project and Department of Chemistry
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
============================================================================
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Received on Mon Apr 18 2005 - 16:53:00 PDT
