AMBER Archive (2008)

Subject: Re: AMBER: amber9 hangas after job submission

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Aug 14 2008 - 07:54:43 CDT

Nothing obvious jumps out at me on this one, though I would note that the
box size is big and the atom count is low, which causes a rather low system
density - down around 0.6 g/cc I would guess. Sometimes low density hits
problems in sander, but this mostly happens in ntp runs as far as I know,
where the box size is shrinking and sander can't keep up with the changes in
memory requirements (this does not happen in pmemd). I would redo the run,
specifying ntpr=1 in the &cntrl section so you can see every result leading
up to the problem, or at least know which step things die in (the default
for ntpr is 50, a lot can go wrong in 50 steps of minimization).
Regards - Bob Duke

----- Original Message -----
From: "Vijay Manickam Achari" <vjrajamany_at_yahoo.com>
To: "Amber Scrops" <amber_at_scripps.edu>
Sent: Thursday, August 14, 2008 2:40 AM
Subject: AMBER: amber9 hangas after job submission

> Dear AMBER experts, I have been trying to run AMBER9 sander, but it did
> not. It stops in the beginning itself.
> Here I give you the output.
>
>
> -------------------------------------------------------
> Amber 9 SANDER 2006
> -------------------------------------------------------
>
> | Run on 08/13/2008 at 17:51:12
> [-O]verwriting output
>
> File Assignments:
> | MDIN: min1-WATER-fix.in
> | MDOUT: min1-WATER-fix-min1.out
> |INPCRD: cello-lyoHIGH.crd
> | PARM: cello-lyoHIGH.top
> |RESTRT: cello-lyoHIGH-min-02.rst
> | REFC: cello-lyoHIGH.crd
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: cello-lyoHIGH-min-01.traj
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
>
> Here is the input file:
>
> betaMaltose-lyo-low water system-FIX the WATER and MINIMIsE the LIPID
> &cntrl
> imin = 1,
> maxcyc = 2500,
> ncyc = 500,
> ntb = 1,
> ntr = 1,
> cut = 10
> /
> Hold the WATER fixed
> 500.0
> RES 257 2056
> END
> END
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags:
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 26.422
> | New format PARM file being parsed.
> | Version = 1.000 Date = 08/12/08 Time = 11:28:22
> NATOM = 35136 NTYPES = 9 NBONH = 26176 MBONA = 9216
> NTHETH = 27648 MTHETA = 12032 NPHIH = 45312 MPHIA = 21248
> NHPARM = 0 NPARM = 0 NNB = 138752 NRES = 5056
> NBONA = 9216 NTHETA = 12032 NPHIA = 21248 NUMBND = 9
> NUMANG = 14 NPTRA = 20 NATYP = 9 NPHB = 1
> IFBOX = 1 NMXRS = 81 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 2334734
> | Hollerith 215874
> | Integer 2211637
> | Max Pairs 20238336
> | nblistReal 421632
> | nblist Int 1948793
> | Total 117685 kbytes
> | 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, iesp = 0
> dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
>
> Energy minimization:
> maxcyc = 2500, ncyc = 500, ntmin = 1
> dx0 = 0.01000, drms = 0.00010
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1
> vdwmeth = 1, eedmeth = 1, netfrc = 0
> Box X = 64.892 Box Y = 169.023 Box Z = 52.843
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 64 NFFT2 = 180 NFFT3 = 54
> Cutoff= 10.000 Tol =0.100E-04
> Ewald Coefficient = 0.27511
> Interpolation order = 4
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> Hold the WATER fixed
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
> GRP 1 RES 257 TO 5056
> Number of atoms in this group = 14400
> ----- END OF GROUP READ -----
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 4800
>
> Sum of charges from parm topology file = 0.00000000
> Forcing neutrality...
>
> --------------------------------------------------------------------------------
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.3338E-14 at 2.509280
> | CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 8858382
> | TOTAL SIZE OF NONBOND LIST = 8858382
>
>
> *****************************************************************************
> It stops there itself.
> I cant figure it out what is the wrong here.
>
> Thanks
>
> Regards
> Vijay.M
>
>
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