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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Received on Wed Aug 19 2009 - 22:23:41 PDT
