AMBER Archive (2009)

Subject: [AMBER] Strange QM/MM Divcon - help me out

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Thu Aug 13 2009 - 10:37:54 CDT


Dear AMBER
I was trying to do simulation of a solvated protein using QM/MM DivCon. I got a strange stimulation of 3 ps of crossed coordinates for atoms, and after 3ps it stopped, becuase a part of the protein moving away.
So, could you check with me my input and comment, please?
MD input, my structure has been minimized and heated using MM AMBER.
------------------------------------------
Title
 &cntrl
  imin= 0,
  irest=1,
  NTX=7,
  ntb=0,
  NTPR=500,
  NTWX=500,
  NTWX=500,
  ntr=0,
  Tempi=300.0,
  Temp0=300.0,
  NTT=3,
  gamma_ln=1.0,
  NTC=2,
  NTF=2,
  cut=12.0,
  nstlim=500000,
  dt=0.001,
  ifqnt=1
 /
 &qmmm
 iqmatoms=1896,1897,1898,1899,1900,1901,1902,1903,1904,1905,1906,
  qmcharge=+1,
  qmtheory=1,
  qmshake=0,
  itrmax=2000,
  scfconv=1.0d-6,
  qm_ewald=1,
  qm_pme=1,  
  qmcut=9,
  idc=1
 /
--------------------------------------

My divcon.in
-------------------------------------
DIRECT CARTESIAN PM3 CHARGE=1.0 &
STANDARD
END_COORD
------------------------------------

Output:
-------------------------
NSTEP =      500   TIME(PS) =      25.500  TEMP(K) =   409.80  PRESS =     0.0
 Etot   =    -38212.8455  EKtot   =     25599.9383  EPtot      =    -63812.7838
 BOND   =       654.7698  ANGLE   =      1619.3184  DIHED      =      1854.3236
 1-4 NB =       636.3054  1-4 EEL =      7274.8455  VDWAALS    =      9086.1196
 EELEC  =    -84940.9996  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 PM3ESCF=         2.5336
 ------------------------------------------------------------------------------

 NSTEP =     1000   TIME(PS) =      26.000  TEMP(K) =   407.45  PRESS =     0.0
 Etot   =    -41640.5897  EKtot   =     25453.0772  EPtot      =    -67093.6669
 BOND   =       977.8399  ANGLE   =      1719.2571  DIHED      =      1920.3964
 1-4 NB =       620.3406  1-4 EEL =      7142.4879  VDWAALS    =      9176.7448
 EELEC  =    -88647.1147  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 PM3ESCF=        -3.6190
 ------------------------------------------------------------------------------

 NSTEP =     1500   TIME(PS) =      26.500  TEMP(K) =   397.85  PRESS =     0.0
 Etot   =    -36544.9324  EKtot   =     24853.5799  EPtot      =    -61398.5124
 BOND   =      1564.5177  ANGLE   =      2170.4825  DIHED      =      1926.9775
 1-4 NB =       645.4201  1-4 EEL =      7108.2898  VDWAALS    =      9307.0854
 EELEC  =    -84163.0386  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 PM3ESCF=        41.7532
 ------------------------------------------------------------------------------

 NSTEP =     2000   TIME(PS) =      27.000  TEMP(K) =   379.86  PRESS =     0.0
 Etot   =    -41064.8006  EKtot   =     23729.4794  EPtot      =    -64794.2800
 BOND   =      2152.1678  ANGLE   =      2255.5364  DIHED      =      1906.0695
 1-4 NB =       607.7985  1-4 EEL =      6956.2110  VDWAALS    =      9637.1547
 EELEC  =    -88257.7439  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 PM3ESCF=       -51.4740
 ------------------------------------------------------------------------------

 NSTEP =     2500   TIME(PS) =      27.500  TEMP(K) =   363.28  PRESS =     0.0
 Etot   =    -37743.4782  EKtot   =     22693.8483  EPtot      =    -60437.3265
 BOND   =      2255.5727  ANGLE   =      2456.9831  DIHED      =      1960.2576
 1-4 NB =       603.0734  1-4 EEL =      6943.3065  VDWAALS    =      9957.3975
 EELEC  =    -84570.1660  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 PM3ESCF=       -43.7513
 ------------------------------------------------------------------------------

 NSTEP =     3000   TIME(PS) =      28.000  TEMP(K) =   354.40  PRESS =     0.0
 Etot   =    -31638.2176  EKtot   =     22139.0181  EPtot      =    -53777.2357
 BOND   =      2203.6831  ANGLE   =      2334.8888  DIHED      =      1949.8389
 1-4 NB =       598.2678  1-4 EEL =      6945.5244  VDWAALS    =     10182.8092
 EELEC  =    -77883.1165  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 PM3ESCF=      -109.1314
 ------------------------------------------------------------------------------

 NSTEP =     3500   TIME(PS) =      28.500  TEMP(K) =   346.34  PRESS =     0.0
 Etot   =    -56733.4934  EKtot   =     21635.5726  EPtot      =    -78369.0660
 BOND   =      2115.6576  ANGLE   =      2348.7200  DIHED      =      1929.8349
 1-4 NB =       611.1261  1-4 EEL =      6984.0194  VDWAALS    =     10480.2072
 EELEC  =   -102848.6746  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 PM3ESCF=        10.0433
 ------------------------------------------------------------------------------

 NSTEP =     4000   TIME(PS) =      29.000  TEMP(K) =   341.54  PRESS =     0.0
 Etot   =    -45994.7521  EKtot   =     21335.8900  EPtot      =    -67330.6421
 BOND   =      2400.8651  ANGLE   =      2328.3901  DIHED      =      1946.3560
 1-4 NB =       620.9436  1-4 EEL =      6943.8657  VDWAALS    =     10496.1736
 EELEC  =    -91926.9660  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 PM3ESCF=      -140.2703
 ------------------------------------------------------------------------------

 Frac coord min, max:   0.183852520823702        1.00008563720960    
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error
---------------------------------------------------------------------------------
Thanks in advance
Bill

      
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