AMBER Archive (2002)

Subject: Re: simulated annealing example

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Wed Jul 10 2002 - 21:59:20 CDT

The error happens when PME (igb=0, default) tries to
read the box information from inpcrd. Since you're
simulating an unsolvated system, you can set igb=3 (no
PME or GB, but a vaccum system with dielectric
constant - epsilon - as a linear function of distance
R). Besides, you can also set dielc=4 (default is 1)
for epsilon=4 * R.

Good luck,

Qing Zhang

--- "Snyder, James" <zyu4_at_cdc.gov> wrote:
> Greetings:
>
> I am attempting to run a simulated annealing calc.
> using the sample input
> file as it EXACTLY appears on page 135 of the AMBER7
> manual. I have
> prepared prmtop and inpcrd files from leap for a
> unsolvated ~6000 atom
> protein, and did not generate a periodic box since
> the apparent plan is to
> do a non-periodic calculation. I have included the
> output file, which
> displays the error message I receive at the bottom.
> If I do create a
> periodic box (using setbox unit vdw), the
> calculation proceeds when the
> resulting prmtop and inpcrd files are used, but the
> program ignores most of
> the settings in the control list, eg. ntb becomes 1
> even though I set it to
> 0 etc. and is obviously not a solution.
>
> ???????
>
> Thank You,
> Jim Snyder
> zyu4_at_cdc.gov
>
>
>
>
-------------------------------------------------------
> Amber 7 SANDER
> Scripps/UCSF 2002
>
>
-------------------------------------------------------
>
> | Wed Jul 10 16:17:53 2002
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: 1fv1_sa.in
>
> | MDOUT: 1fv1_sa.out
>
> |INPCRD: 1fv1_sa.crd
>
> | PARM: 1fv1_sa.top
>
> |RESTRT: 1fv1_sa.rst
>
> | REFC: 1fv1_sa.crd
>
> | MDVEL: mdvel
>
> | MDEN: mden
>
> | MDCRD: 1fv1_sa.traj
>
> |MDINFO: mdinfo
>
> |INPDIP: inpdip
>
> |RSTDIP: rstdip
>
>
>
> Here is the input file:
>
> 15ps simulated annealing protocol
>
> &cntrl
>
> nstlim=15000, ntt=1, (time limit, temp.
> control)
>
> scee=1.2, (scee holds the 1-4 scale factor)
>
> ntpr=500, pencut=0.1, (control of printout)
>
> ipnlty=1, nmropt=1, (NMR penalty function
> options)
>
> vlimit=10, (prevent bad temp. jumps)
>
> ntb=0, (non-periodic simulation)
>
> &end
>
> #
>
> # Simple simulated annealing algorithm:
>
> #
>
> # from steps 0 to 1000: raise target
> temperature 10->1200K
>
> # from steps 1000 to 3000: leave at 1200K
>
> # from steps 3000 to 15000: re-cool to low
> temperatures
>
> #
>
> &wt type='TEMP0', istep1=0,istep2=1000,value1=10.,
>
> value2=1200., &end
>
> &wt type='TEMP0', istep1=1001, istep2=3000,
> value1=1200.,
>
> value2=1200.0, &end
>
> &wt type='TEMP0', istep1=3001, istep2=15000,
> value1=0.,
>
> value2=0.0, &end
>
> #
>
> # Strength of temperature coupling:
>
> #
>
> # steps 0 to 3000: tight coupling for heating
> and equilibration
>
> # steps 3000 to 11000: slow cooling phase
>
> # steps 11000 to 13000: somewhat faster cooling
>
> # steps 13000 to 15000: fast cooling, like a
> minimization
>
> #
>
> &wt type='TAUTP', istep1=0,istep2=3000,value1=0.2,
>
> value2=0.2, &end
>
> &wt type='TAUTP',
> istep1=3001,istep2=11000,value1=4.0,
>
> value2=2.0, &end
>
> &wt type='TAUTP',
> istep1=11001,istep2=13000,value1=1.0,
>
> value2=1.0, &end
>
> &wt type='TAUTP',
> istep1=13001,istep2=14000,value1=0.5,
>
> value2=0.5, &end
>
> &wt type='TAUTP',
> istep1=14001,istep2=15000,value1=0.05,
>
> value2=0.05, &end
>
>
>
> #
>
> # "Ramp up" the restraints over the first 3000
> steps:
>
> #
>
> &wt type='REST', istep1=0,istep2=3000,value1=0.1,
>
> value2=1.0, &end
>
> &wt type='REST',
> istep1=3001,istep2=15000,value1=1.0,
>
> value2=1.0, &end
>
>
>
> &wt type='END' &end
>
> LISTOUT=POUT
>
> DISANG=RST.f
>
>
>
----------------------------------------------------------------------------
> ----
> 1. RESOURCE USE:
>
----------------------------------------------------------------------------
> ----
>
> | Flags: SGIFFT MEM_ALLOC MPI RLE ROWAT HAS_FTN_ERFC
>
> getting new box info from bottom of inpcrd
> | peek_ewald_inpcrd: Box info not found in inpcrd
> compute_nfft: failed to get good fft array size
> x = 4.93287768640256299E+24
>
=== message truncated ===

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