AMBER Archive (2005)

Subject: Re: AMBER: lastrst

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Feb 22 2005 - 20:36:00 CST

Dear Julie,

I have run a minimisation with the same input .in file u used (except with
bellymask='!:1-8' line for a 4X4 RNA structure solvated in water). I did
not have any problem with the simulation. In the amber mailing list, they
are suggesting to increase the value of lastrst, but you say you have
already done this by increasing lastrst upto 10e+32. If the problem is
not with the value of lastrst, maybe u should test minimizing some part of
your system (I assume it is a big structure).

I also did the same minimization with the suggested ntr=1. The final
energy results of the one with ibelly=1 and ntr=1 are different. Here are
the final outputs:

------ with ibelly=1 -------
 NSTEP ENERGY RMS GMAX NAME NUMBER
 1000 -3.2844E+04 5.0508E-01 7.9498E+00 O 3976

BOND = 1092.0103 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 1024.2103 EEL = -34960.4747 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
------ with ntr=1 ------
 NSTEP ENERGY RMS GMAX NAME NUMBER
 1000 -2.5772E+04 4.1126E-01 7.9888E+00 C4' 169

BOND = 1102.2317 ANGLE = 76.6238 DIHED = 168.5913
VDWAALS = 1048.6803 EEL = -27055.6050 HBOND = 0.0000
1-4 VDW = 67.0672 1-4 EEL = -1327.8012 RESTRAINT = 148.6915
EAMBER = -25920.2118
------------------------

Good luck.

On Tue, 22 Feb 2005, Stern, Julie wrote:

> I keep getting the following error message no matter how large I make
> lastrst
> in my minimization file as if it weren't reading what I'm setting. I even
> went as high as 10e+32.
>
> Any suggestions?
>
>
> Exceeding lastrst in get_stack
> lastrst = 3564
> top_stk= 0
> isize = 22133
> request= 22133
> Increase lastrst in the &cntrl namelist
>
> Minimization intpminimization
> &cntrl
> imin=1,
> ncyc=250,
> maxcyc=1000,
> lastrst=8000000,
> lastist=8000000,
> ntf=1,
> ntc=1,
> ntpr=10,
> igb=0,
> ntb=1,
> cut=3.0,
> ibelly=1,
> bellymask='!@SA',
> &end
>
>
> From the minimization output:
>
> | Memory Use Allocated
> | Real 89727
> | Hollerith 69
> | Integer 42095
> | Max Pairs 55
> | Max Rstack 3564
> | Max Istack 55
> | Total 893 kbytes
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  - http://www.pas.rochester.edu/~yildirim/                     -
  ---------------------------------------------------------------

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