End-point simulations were just fine. I didn't see any problem.
On Mon, May 17, 2010 at 12:45 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
>
--
Best,
InSuk Joung
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 17 2010 - 10:00:07 PDT
