AMBER Archive (2003)

Subject: Re: Problem with Snader

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Sat Jun 28 2003 - 09:53:59 CDT

lastist corresponds to MAX_ISTACK (see comments in sizes.h). it's a nice
change since amber7 that you don't have to recompile sander every time when
this happens. you need only set lastist to a larger integer (>2035416, quoted
from your output).

On Saturday 28 June 2003 09:17, Frederico.Miranda_at_ibmb.uib.no wrote:
> Hello, I tried a minimization in Sander and got this output:
>
> _______________________________
>
>
>
> -------------------------------------------------------
> Amber 7 SANDER Scripps/UCSF 2002
> -------------------------------------------------------
>
> | Run on Mon Apr 14 17:27:43 1952
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: /work/miranda/pidimer_min.in
> | MDOUT: /work/miranda/pidimer_min.out
> |INPCRD: /work/miranda/pidimer.inpcrd
> | PARM: /work/miranda/pidimer.prmtop
> |RESTRT: /work/miranda/pidimer.mincrd
> | REFC: /work/miranda/pidimer.inpcrd
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> |MDINFO: /work/miranda/pidimer_min.info
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
> Here is the input file:
>
> &cntrl
> igb = 0, ntb = 1, ntpr = 50,
>
> cut = 9.0,
>
> ibelly = 0, ntr = 0,
>
> imin = 1, maxcyc = 1000, ncyc = 1000,
> &end
>
> ---------------------------------------------------------------------------
>----- 1. RESOURCE USE:
> ---------------------------------------------------------------------------
>-----
>
> | Flags: MEM_ALLOC MPI RLE ROWAT
>
> getting new box info from bottom of inpcrd
>
> | peek_ewald_inpcrd: Box info found
> | New format PARM file being parsed.
> | Version = 1.000 Date = 06/28/03 Time = 12:54:43
>
> NATOM = 84809 NTYPES = 19 NBONH = 77456 MBONA = 7516
> NTHETH = 16478 MTHETA = 10174 NPHIH = 29868 MPHIA = 17886
> NHPARM = 0 NPARM = 0 NNB = 174347 NRES = 24329
> NBONA = 7516 NTHETA = 10174 NPHIA = 17886 NUMBND = 48
> NUMANG = 96 NPTRA = 34 NATYP = 34 NPHB = 1
> IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
>
> | Memory Use Allocated
> | Real 6818828
> | Hollerith 533185
> | Integer 5252296
> | Max Pairs 4031456
> | Max Rstack 2000000
> | Max Istack 2000000
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: RECTILINEAR
>
> ---------------------------------------------------------------------------
>----- 2. CONTROL DATA FOR THE RUN
> ---------------------------------------------------------------------------
>-----
>
>
>
> General flags:
> imin = 1, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
> 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
> Potential function:
> ntf = 1, ntb = 1, igb = 0, nsnb =
> 25 ipol = 0, gbsa = 0
> dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 1000, ncyc = 1000, ntmin = 1
> dx0 = 0.01000, dxm = 0.50000, drms = 0.00010
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1 vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc =
> 1 Box X = 95.869 Box Y = 112.893 Box Z = 99.514
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 96 NFFT2 = 120 NFFT3 = 100
> Cutoff= 9.000 Tol =0.100E-04
> Ewald Coefficient = 0.30768
> Interpolation order = 4
>
> | PLEVEL = 1: runmd parallelization, no EKCMR
>
> Exceeding lastist in get_istack
> lastist = 2000000
> top_stk= 1950607
> isize = 84809
> request= 2035416
> Increase lastist in the &cntrl namelist
>
> _______________________________
>
> For what I understand, there is a problem with the value called lastist,
> but I don't know what that means. Could someone help me with this please?
> Thank you. 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790