On Sat, Jun 26, 2010, Jagdeesh C wrote:
> Dear Amber Users,
>
> I have provided the following input for minimization. I am getting a
> segmentation fault error. Can someone please help explain me what might be
> the reason?
>
>
> Many thanks,
> Jagdeesh
> *
> INPUT*
> minimize_polak
> &cntrl
> imin=1, ntmin=3,
> irest=0, ntx=1,
> maxcyc=1000,
> cut=8.0,ntb=2,
> ntpr=1,
> ntp =1,
> /
> &lmod
> xmin_method = "PRCG",
> /
Setting ntb=2, ntp=1 doesn't make any sense with minimization; see if setting
ntb=1 helps. Let us know what happens--if this is indeed the problem, it's
a bug we should fix.
Otherwise: what happens if you set ntmin to 1 or 2?
....dac
> *
> OUTPUT*
>
> Segmentation fault
> *
> OUTPUT FILE*
>
> File Assignments:
> | MDIN: minx_02.in
>
> | MDOUT:
> minx2_143d.out
> |INPCRD:
> min_143dx.rst
> | PARM:
> 143d_sol.prmtop
> |RESTRT:
> min_143dx2.rst
> | REFC:
> min_143dx.rst
> | MDVEL:
> mdvel
> | MDEN:
> mden
> | MDCRD:
> mdcrd
> |MDINFO:
> mdinfo
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
> |INPTRA:
> inptraj
> |
>
> Here is the input file:
>
> polak
>
> &cntrl
>
> imin=1,
> ntmin=3,
> irest=0,
> ntx=1,
> maxcyc=1000,
>
> cut=8.0,ntb=2,
>
> ntpr=1,
>
> ntp
> =1,
> /
>
> &lmod
>
> xmin_method =
> "PRCG",
> /
>
>
> --------------------------------------------------------------------------------
> 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 = 23.842
> | New format PARM file being parsed.
> | Version = 1.000 Date = 06/01/10 Time = 11:08:47
> NATOM = 12646 NTYPES = 17 NBONH = 12160 MBONA = 524
> NTHETH = 592 MTHETA = 812 NPHIH = 1260 MPHIA = 1431
> NHPARM = 0 NPARM = 0 NNB = 19884 NRES = 4013
> NBONA = 524 NTHETA = 812 NPHIA = 1431 NUMBND = 36
> NUMANG = 68 NPTRA = 41 NATYP = 27 NPHB = 1
> IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 843928
> | Hollerith 79891
> | Integer 347428
> | Max Pairs 4215333
> | nblistReal 151752
> | nblist Int 543090
> | Total 28035 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: TRUNCATED OCTAHEDRON
>
> --------------------------------------------------------------------------------
> 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 = 1, 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 = 2, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 1000, ncyc = 10, ntmin = 3
> dx0 = 0.01000, drms = 0.00010
>
> LMOD:
> xmin_method = PRCG
> matrix_vector_product_method = forward finite difference
> xmin_verbosity = 0
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme
> = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 0
> Box X = 58.401 Box Y = 58.401 Box Z = 58.401
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> NFFT1 = 60 NFFT2 = 60 NFFT3 = 60
> Cutoff= 8.000 Tol =0.100E-04
> Ewald Coefficient = 0.34864
> Interpolation order = 4
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 3970
>
> Sum of charges from parm topology file = 0.00000006
> Forcing neutrality...
>
> --------------------------------------------------------------------------------
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> LMOD XMIN Minimization.
> ---------------------------------------------------
> 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 = 0.3140E-14 at 2.473100
> | CHECK d/dx switch(x): max rel err = 0.8129E-11 at 2.782960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 2193879
> | TOTAL SIZE OF NONBOND LIST = 2193879
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -3.8657E+04 0.0000E+00 3.9990E+01 O 4625
>
> BOND = 32.6084 ANGLE = 194.8141 DIHED =
> 419.5199
> VDWAALS = 1860.6096 EEL = -39348.9396 HBOND =
> 0.0000
> 1-4 VDW = 174.0771 1-4 EEL = -1989.1934 RESTRAINT =
> 0.0000
> (END)
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> http://lists.ambermd.org/mailman/listinfo/amber
--
================================================================
David A. Case | email:
BioMaPS Institute and Dept. of | case.biomaps.rutgers.edu
Chemistry & Chemical Biology | fax: +1-732-445-5958
Rutgers University | phone: +1-732-445-5885
610 Taylor Rd. |
Piscataway, NJ 08854-8087 USA | http://casegroup.rutgers.edu
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Received on Sat Jun 26 2010 - 16:00:03 PDT
