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",
/
*
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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Received on Sat Jun 26 2010 - 03:30:03 PDT
