Hi Insuk,
One initial question. Have you tried running QM/MM simulations of your end
points without the thermodynamic integration? Does this work correctly?
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of InSuk Joung
> Sent: Monday, May 17, 2010 9:27 AM
> To: Amber Mailing List
> Subject: [AMBER] QMMM and Thermodynamic integration
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 17 2010 - 10:00:04 PDT
