Dear Amer users,
I am minimizing CI2 protein in water box . I am
getting LINMIN failure. Can anybody solve the problem. Here is the .out
file.
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 05/18/2011 at 18:02:37
File Assignments:
| MDIN: min3.in
| MDOUT:
min3.out
|INPCRD:
min2.rst
| PARM:
CI2_wat.top
|RESTRT:
min3.rst
| REFC:
CI2_wat.crd
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
min3.crd
|MDINFO: min3.info
|INPDIP:
inpdip
|RSTDIP:
rstdip
Here is the input file:
shake, belly minimization of hydrogens in
waters)
&cntrl
imin = 1, maxcyc = 1000, ncyc = 250, ntr = 1, ntb
=1,
&end
Restrain the heavy
atoms
20.0
RES 1
3622
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
MPI
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 = 23.125
| New format PARM file being parsed.
| Version = 1.000 Date = 05/14/11 Time = 11:02:27
NATOM = 11722 NTYPES = 16 NBONH = 11215 MBONA = 512
NTHETH = 1251 MTHETA = 694 NPHIH = 2270 MPHIA = 1754
NHPARM = 0 NPARM = 0 NNB = 20082 NRES = 3622
NBONA = 512 NTHETA = 694 NPHIA = 1754 NUMBND = 35
NUMANG = 73 NPTRA = 38 NATYP = 25 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 870447
| Hollerith 73956
| Integer 352451
| Max Pairs 325611
| nblistReal 140664
| nblist Int 466138
| Total 12657 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 = 8.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 1000, ncyc = 250, 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 = 55.447 Box Y = 59.373 Box Z = 46.250
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 60 NFFT2 = 60 NFFT3 = 48
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Restrain the heavy atoms
GROUP 1 HAS HARMONIC CONSTRAINTS 20.00000
GRP 1 RES 1 TO 3622
Number of atoms in this group = 11722
----- 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: 3556
| Atom division among processors:
| 0 754 1465 2197 2929 3661 4393 5125
| 5857 6589 7321 8053 8785 9517 10249 10981
| 11722
Sum of charges from parm topology file = -0.00000393
Forcing neutrality...
| Running AMBER/MPI version on 16 nodes
--------------------------------------------------------------------------------
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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 134011
| TOTAL SIZE OF NONBOND LIST = 1970608
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.0888E+05 2.4189E+01 1.2558E+02 O 6974
BOND = 4063.1349 ANGLE = 103.0332 DIHED =
578.6856
VDWAALS = 10141.2213 EEL = -66566.0018 HBOND =
0.0000
1-4 VDW = 223.2008 1-4 EEL = 2516.7761 RESTRAINT =
257820.2884
EAMBER = -48939.9500
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -3.2370E+03 1.2746E+01 5.7909E+02 CB 412
BOND = 3342.8149 ANGLE = 471.7360 DIHED =
580.8015
VDWAALS = 5657.1677 EEL = -55705.4520 HBOND =
0.0000
1-4 VDW = 284.7907 1-4 EEL = 2508.6552 RESTRAINT =
39622.4574
EAMBER = -42859.4860
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -3.6835E+04 5.5712E+00 7.0761E+02 CG 910
BOND = 2560.2062 ANGLE = 149.0582 DIHED =
581.7071
VDWAALS = 3904.3631 EEL = -50945.8634 HBOND =
0.0000
1-4 VDW = 221.2294 1-4 EEL = 2510.1657 RESTRAINT =
4183.9320
EAMBER = -41019.1336
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -3.8533E+04 1.4934E+00 1.9911E+02 CG 910
BOND = 2391.4670 ANGLE = 105.0015 DIHED =
579.9014
VDWAALS = 3691.9890 EEL = -50196.7134 HBOND =
0.0000
1-4 VDW = 220.7017 1-4 EEL = 2507.8363 RESTRAINT =
2166.6877
EAMBER = -40699.8165
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -3.8660E+04 1.8256E-01 1.2322E+01 O 6092
BOND = 2370.4854 ANGLE = 103.8577 DIHED =
579.8497
VDWAALS = 3651.0640 EEL = -50026.9093 HBOND =
0.0000
1-4 VDW = 220.6916 1-4 EEL = 2508.0004 RESTRAINT =
1932.5214
EAMBER = -40592.9605
NSTEP ENERGY RMS GMAX NAME NUMBER
250 -3.8674E+04 2.0850E-01 1.5689E+01 H1 1107
BOND = 2368.3429 ANGLE = 103.8635 DIHED =
579.8212
VDWAALS = 3642.7160 EEL = -49987.4908 HBOND =
0.0000
1-4 VDW = 220.7296 1-4 EEL = 2508.1185 RESTRAINT =
1890.1562
EAMBER = -40563.8993
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -3.8675E+04 4.8025E-03 3.4253E-01 H2 6094
BOND = 2366.6087 ANGLE = 103.8441 DIHED =
579.8063
VDWAALS = 3640.2438 EEL = -49972.5748 HBOND =
0.0000
1-4 VDW = 220.7371 1-4 EEL = 2508.1068 RESTRAINT =
1878.0790
EAMBER = -40553.2280
NSTEP ENERGY RMS GMAX NAME NUMBER
350 -3.8675E+04 1.6858E-03 9.2576E-02 O 6101
BOND = 2366.6249 ANGLE = 103.8454 DIHED =
579.8070
VDWAALS = 3640.3510 EEL = -49972.7146 HBOND =
0.0000
1-4 VDW = 220.7387 1-4 EEL = 2508.1051 RESTRAINT =
1878.0879
EAMBER = -40553.2425
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -3.8675E+04 3.0836E-03 2.9469E-01 CG 910
BOND = 2366.6293 ANGLE = 103.8451 DIHED =
579.8073
VDWAALS = 3640.3825 EEL = -49972.7360 HBOND =
0.0000
1-4 VDW = 220.7392 1-4 EEL = 2508.1047 RESTRAINT =
1878.0741
EAMBER = -40553.2282
NSTEP ENERGY RMS GMAX NAME NUMBER
450 -3.8675E+04 8.9252E-04 6.0523E-02 CG 910
BOND = 2366.6342 ANGLE = 103.8454 DIHED =
579.8074
VDWAALS = 3640.3865 EEL = -49972.7419 HBOND =
0.0000
1-4 VDW = 220.7390 1-4 EEL = 2508.1044 RESTRAINT =
1878.0707
EAMBER = -40553.2249
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -3.8675E+04 8.4335E-04 6.9623E-02 CG 910
BOND = 2366.6360 ANGLE = 103.8454 DIHED =
579.8075
VDWAALS = 3640.3907 EEL = -49972.7432 HBOND =
0.0000
1-4 VDW = 220.7391 1-4 EEL = 2508.1043 RESTRAINT =
1878.0662
EAMBER = -40553.2202
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -3.8675E+04 5.8685E-04 4.6561E-02 CG 910
BOND = 2366.6387 ANGLE = 103.8456 DIHED =
579.8076
VDWAALS = 3640.4001 EEL = -49972.7419 HBOND =
0.0000
1-4 VDW = 220.7391 1-4 EEL = 2508.1040 RESTRAINT =
1878.0525
EAMBER = -40553.2067
.... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO
*****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
570 -3.8675E+04 4.0116E-04 3.0542E-02 CG 910
BOND = 2366.6385 ANGLE = 103.8455 DIHED =
579.8076
VDWAALS = 3640.4034 EEL = -49972.7439 HBOND =
0.0000
1-4 VDW = 220.7392 1-4 EEL = 2508.1040 RESTRAINT =
1878.0503
EAMBER = -40553.2057
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.01 ( 0.05% of Total)
| Build the list 0.21 (61.23% of List )
| Other 0.13 (38.77% of List )
| List time 0.35 ( 3.25% of Nonbo)
| Short_ene time 2.40 (79.89% of Direc)
| Other 0.60 (20.11% of Direc)
| Direct Ewald time 3.00 (29.01% of Ewald)
| Adjust Ewald time 0.05 ( 0.47% of Ewald)
| Self Ewald time 0.00 ( 0.03% of Ewald)
| Fill Bspline coeffs 0.21 ( 8.40% of Recip)
| Fill charge grid 0.14 ( 5.35% of Recip)
| Scalar sum 0.23 ( 9.00% of Recip)
| Grad sum 0.16 ( 6.23% of Recip)
| FFT back comm time 0.92 (61.27% of FFT t)
| Other 0.58 (38.73% of FFT t)
| FFT time 1.50 (59.29% of Recip)
| Other 0.30 (11.73% of Recip)
| Recip Ewald time 2.53 (24.42% of Ewald)
| Force Adjust 4.13 (39.89% of Ewald)
| Virial junk 0.64 ( 6.15% of Ewald)
| Start sycnronization 0.00 ( 0.01% of Ewald)
| Other 0.00 ( 0.03% of Ewald)
| Ewald time 10.35 (96.74% of Nonbo)
| Other 0.00 ( 0.01% of Nonbo)
| Nonbond force 10.70 (68.21% of Force)
| Bond/Angle/Dihedral 0.10 ( 0.62% of Force)
| FRC Collect time 1.50 ( 9.59% of Force)
| Other 3.39 (21.58% of Force)
| Force time 15.69 (100.0% of Runmd)
| Runmd Time 15.69 (97.05% of Total)
| Other 0.47 ( 2.90% of Total)
| Total time 16.16 (100.0% of ALL )
| Highest rstack allocated: 79161
| Highest istack allocated: 1953
| Job began at 18:02:37.613 on 05/18/2011
| Setup done at 18:02:37.835 on 05/18/2011
| Run done at 18:02:53.779 on 05/18/2011
| wallclock() was called 25146 times
R.Dhilip kumar
Computational Biophysics Lab
Department of Biotechnology
IIT Madras
Chennai-600036
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Received on Wed May 18 2011 - 06:30:02 PDT
