Hello.
When I used AMBER10 with input file below,I met error message...
TESTING RELATIVE ERRORover r ranging from 0.0 to cutoff.
How can I pass the this error message?????
I need your help~~
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
Run on 07/08/2013 at 17:38:27
[-O]verwriting output
FileAssignments:
MDIN: min1.in
MDOUT: min1.out
INPCRD:11mersol.inpcrd
PARM: 11mersol.prmtop
RESTRT:min1.restrt
REFC: 11mersol.inpcrd
MDVEL: mdvel
MDEN: mden
MDCRD: mdcrd
MDINFO:mdinfo
INPDIP:inpdip
RSTDIP:rstdip
Here is the input file:
11merminimization
&cntrl
imin = 1,
maxcyc = 2000,
ncyc = 1000,
ntb = 1,
ntr = 1,
cut = 10
/
Holdthe DNA fixed
500.0
RES1 22
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
Largestsphere to fit in unit cell has radius = 30.160
New format PARM file being parsed.
Version = 1.000 Date = 01/22/13 Time =15:24:05
NATOM = 20250 NTYPES = 18 NBONH = 19786 MBONA = 496
NTHETH = 588 MTHETA = 762 NPHIH = 1260 MPHIA = 1344
NHPARM = 0 NPARM = 0 NNB = 29924 NRES = 6554
NBONA = 496 NTHETA = 762 NPHIA = 1344 NUMBND = 39
NUMANG = 76 NPTRA = 42 NATYP = 28 NPHB = 1
IFBOX = 1 NMXRS = 33 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Memory Use Allocated
Real 1380212
Hollerith 128056
Integer 510434
Max Pairs 11664000
nblistReal 243000
nblist Int 807800
Total 63893 kbytes
Duplicated 0 dihedrals
Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
Generalflags:
imin = 1, nmropt = 0
Natureand format of input:
ntx = 1, irest = 0, ntrx = 1
Natureand 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
Potentialfunction:
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
Frozenor restrained atoms:
ibelly = 0, ntr = 1
Energyminimization:
maxcyc = 2000, ncyc = 1000, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewaldparameters:
verbose = 0, ew_type = 0,nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 60.320 Box Y = 68.060 Box Z = 61.996
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 60 NFFT2 = 72 NFFT3 = 64
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 DNA fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
GRP 1RES 1 TO 22
Number of atoms in this group = 694
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point watersfound: 6512
Sum of charges from parm topology file= 0.00000013
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch usingCUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTINGRELATIVE ERROR over r ranging from 0.0 to cutoff
CHECK switch(x): max rel err = 0.3338E-14 at 2.509300
CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040
---------------------------------------------------
Local SIZE OF NONBOND LIST = 5997049
TOTAL SIZE OF NONBOND LIST = 5997049
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaNQ NaNQ 2.5067E+06 C2' 690
BOND = 547139.9071 ANGLE = 2188.4961 DIHED = 504.1794
VDWAALS = NaNQ EEL = NaNQ HBOND = 0.0000
1-4 VDW = 680.4379 1-4 EEL = -2982.8481 RESTRAINT = 0.0000
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jeonsunny님의 블로그
안녕하세요.
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Received on Mon Jul 08 2013 - 23:30:03 PDT
