Hi,
I have a problem in transforming a molecule from MM to QM.
I don't see a problem with a simple organic molecules but I see a problem
with this specific case. The molecule that undergoes the transformation is
magnesium hexahydrate(Mg(H_2O)_6^2+). The molecules is solvated in SPC/E
water.
Here are my input files for MD.
MM
&cntrl
imin=0, ntx=1, ntpr=10, ntwr=0, ntwx=10,
nscm=10000,
ntf=2, ntc=2, tol=1d-7,
ntb=2, ntp=1, taup=1.0,
ntt=3, gamma_ln = 10, temp0=298.0,
nstlim=5000, t=0.0, dt=0.002,
cut=9.0,
icfe = 1, clambda = 0.9, klambda = 2,
&end
QM
&cntrl
imin=0, ntx=1, ntpr=10, ntwr=0, ntwx=10,
nscm=10000,
ntf=2, ntc=2, tol=1d-7,
ntb=2, ntp=1, taup=1.0,
ntt=3, gamma_ln = 10, temp0=298.0,
nstlim=5000, t=0.0, dt=0.002,
cut=9.0,
icfe = 1, clambda = 0.9, klambda = 2,
ifqnt=1,
&end
&qmmm
qmmask=':1-7', qmcharge=2, qm_theory='PM3',
&end
After a minimization, I ran a short MD with the input files above. However,
it fails for an unknown reason (maybe vlimit problem).
The output files shows:
This is the very last lines of the MM-side output
...
vlimit exceeded for step 384; vmax = 22.9514
NSTEP = 390 TIME(PS) = 0.780 TEMP(K) = 438.51 PRESS =
-141.7
Etot = -6510.1865 EKtot = 2325.3637 EPtot =
-8835.5502
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1656.2544
EELEC = -10426.5330 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 34.0342
EKCMT = 830.1517 VIRIAL = 950.4602 VOLUME =
39315.8198
Density =
0.6775
Ewald error estimate: 0.1551E-01
------------------------------------------------------------------------------
vlimit exceeded for step 395; vmax = 20.6629
NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 424.69 PRESS =
-264.4
Etot = -6678.8985 EKtot = 2252.0310 EPtot =
-8930.9294
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1638.8015
EELEC = -10457.3070 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 38.9671
EKCMT = 857.6500 VIRIAL = 1082.0626 VOLUME =
39307.4472
Density =
0.6776
Ewald error estimate: 0.1662E-01
------------------------------------------------------------------------------
vlimit exceeded for step 403; vmax = 21.6259
vlimit exceeded for step 405; vmax = 21.0006
NSTEP = 410 TIME(PS) = 0.820 TEMP(K) = 478.56 PRESS =
-149.9
Etot = -6368.8503 EKtot = 2537.7101 EPtot =
-8906.5604
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1648.1926
EELEC = -10428.8965 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 17.2499
EKCMT = 886.6024 VIRIAL = 1013.7637 VOLUME =
39300.3313
Density =
0.6778
Ewald error estimate: 0.1745E-01
------------------------------------------------------------------------------
vlimit exceeded for step 410; vmax = 21.7172
NSTEP = 420 TIME(PS) = 0.840 TEMP(K) = 440.89 PRESS =
-231.7
Etot = -6589.7715 EKtot = 2337.9448 EPtot =
-8927.7163
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1635.9136
EELEC = -10436.3811 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 23.6872
EKCMT = 866.5756 VIRIAL = 1063.1903 VOLUME =
39296.4107
Density =
0.6778
Ewald error estimate: 0.1736E-01
------------------------------------------------------------------------------
vlimit exceeded for step 420; vmax = 20.5795
vlimit exceeded for step 421; vmax = 21.0169
This is from QM-side output,
...
NSTEP = 390 TIME(PS) = 0.780 TEMP(K) = 316.30 PRESS =
-141.7
Etot = -7158.2642 EKtot = 1677.2860 EPtot =
-8835.5502
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1656.2544
EELEC = -10426.5330 EHBOND = 0.0000 RESTRAINT =
0.0000
PM3ESCF= -65.2716
DV/DL = 34.0342
EKCMT = 830.1517 VIRIAL = 950.4602 VOLUME =
39315.8198
Density =
0.6775
Ewald error estimate: 0.1551E-01
------------------------------------------------------------------------------
NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 329.82 PRESS =
-264.4
Etot = -7181.9535 EKtot = 1748.9759 EPtot =
-8930.9294
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1638.8015
EELEC = -10457.3070 EHBOND = 0.0000 RESTRAINT =
0.0000
PM3ESCF= -112.4239
DV/DL = 38.9671
EKCMT = 857.6500 VIRIAL = 1082.0626 VOLUME =
39307.4472
Density =
0.6776
Ewald error estimate: 0.1662E-01
------------------------------------------------------------------------------
NSTEP = 410 TIME(PS) = 0.820 TEMP(K) = 336.59 PRESS =
-149.9
Etot = -7121.6759 EKtot = 1784.8845 EPtot =
-8906.5604
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1648.1926
EELEC = -10428.8965 EHBOND = 0.0000 RESTRAINT =
0.0000
PM3ESCF= -125.8565
DV/DL = 17.2499
EKCMT = 886.6024 VIRIAL = 1013.7637 VOLUME =
39300.3313
Density =
0.6778
Ewald error estimate: 0.1745E-01
------------------------------------------------------------------------------
NSTEP = 420 TIME(PS) = 0.840 TEMP(K) = 327.39 PRESS =
-231.7
Etot = -7191.6108 EKtot = 1736.1055 EPtot =
-8927.7163
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1635.9136
EELEC = -10436.3811 EHBOND = 0.0000 RESTRAINT =
0.0000
PM3ESCF= -127.2489
DV/DL = 23.6872
EKCMT = 866.5756 VIRIAL = 1063.1903 VOLUME =
39296.4107
Density =
0.6778
Ewald error estimate: 0.1736E-01
------------------------------------------------------------------------------
I notice several weird things here. First, vlimit warnings only show up in
MM-side output. Second, themperature is not regulated correctly. I looked
at the trajectory of the simulation and found that the waters of magnesium
hexahydrate moves really fast indeed.
I would appreciate if anyone can advise on this issue. Thank you!
--
Best,
InSuk Joung
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Received on Mon May 17 2010 - 09:30:08 PDT
