As everyone suggested restraints might be the cause, I am retrying with the
restraints removed. It will take few days to get near 800 ps as it is a
large QM region.
I will also try using semiempirical Hamiltonian PM6 and hope that it helps.
On Wed, Mar 27, 2019 at 3:24 AM Goetz, Andreas <agoetz.sdsc.edu> wrote:
> The Gaussian output has an entry “Atoms too close”. This means that part
> of your QM region has a bad geometry. Given that your first few hundred
> steps were stable, this must have happened at some point during your
> trajectory, perhaps because of your restraints. As a consequence, Gaussian
> is probably not able to optimize the correct ground state electron density,
> which results in bad forces both for the QM region and the classical atoms
> that are coupled via the QM/MM Hamiltonian (within your QM cutoff, as you
> observe).
>
> You have to be careful equilibrating QM/MM calculations. Perhaps try a
> semiempirical Hamiltonian like PM6 first to see how the system behaves.
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> > On Mar 26, 2019, at 6:33 AM, Abhilash J <md.scfbio.gmail.com> wrote:
> >
> > Yes, The temperature is increasing too rapidly. I did not notice that
> > earlier. Thanks for pointing it out. But it was stable till 0.796 ps.
> > I don't know what can caused the thermostat to fail. It did not fail in
> the
> > last run of (1 ps) the same complex (that too was QM).
> > One interesting point is that the erratic movement of atoms happens in
> the
> > region described in the 10A cut sphere region of QM. Rest of the protein
> > atoms are fine.
> > So I think it might be linked to QM part.
> >
> > This is the active site containing domain part of a larger protein. I
> have
> > run over 500 ns with the complete protein, and it runs fine using MM.
> > Current complex (active site domain part) has some active site residues,
> > ATP, MG2+, K+ ions and catalytic water in QM region. Rest of the protein,
> > water and ions are treated as MM.
> > One thing i can try is to remove the restraints on the initial amino
> acids
> > of the protein and try this again. I will try this.
> > I think i should point out that I am using sander with Gaussian
> interface.
> > In case it helps.
> >
> >
> >
> > On Tue, Mar 26, 2019 at 4:09 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> How does it go without QMM?
> >>
> >> Bill
> >>
> >>
> >> On 3/26/19 2:45 AM, Szymon Żaczek wrote:
> >>> Dear Abhilash,
> >>>
> >>> please, have a look at temperatures in your system: Starting from
> >>> 798th step onwards it is rising very rapidly., much above the defined
> >>> 300 K. This may be caused by a plethora of issues but generally it
> >>> means that your system is unstable. Restraint energy in your system is
> >>> pretty high comparing to the restraint value that you defined - it may
> >>> be the main cause of your system's instability.
> >>>
> >>> Kind regards,
> >>> Szymon
> >>>
> >>> wt., 26 mar 2019 o 10:27 Abhilash J <md.scfbio.gmail.com> napisał(a):
> >>>> Hi everyone,
> >>>>
> >>>> I am trying QMMM for a protein ATP complex. After 1.798 ps the
> >> system
> >>>> suddenly shows vmax error
> >>>> vlimit exceeded for step 798; vmax = **********
> >>>>
> >>>> When i googled the error i found that it occurs when there is atom
> >>>> overlap. So i checked the trajectory. The atoms in the region around
> >> the QM
> >>>> region (seemingly 10A, probably due to cut variable) suddenly move
> away
> >>>> from each other. And Gaussian shows error (attached below)
> >>>> I cannot understand why this is so.
> >>>> * The AMBER output file look like this:*
> >>>>
> =======================================================================
> >>>> NSTEP = 796 TIME(PS) = 0.796 TEMP(K) = 283.32 PRESS
> =
> >>>> 0.0
> >>>> Etot = -2958635.1773 EKtot = 35534.3457 EPtot =
> >>>> -2994169.5230
> >>>> BOND = 23904.6935 ANGLE = 2717.0388 DIHED =
> >>>> 4447.2846
> >>>> 1-4 NB = 1264.0951 1-4 EEL = 14929.0965 VDWAALS =
> >>>> 20957.1806
> >>>> EELEC = -192019.8681 EHBOND = 0.0000 RESTRAINT =
> >>>> 61.9493
> >>>> EXTERNESCF= -2870430.9932
> >>>> EAMBER (non-restraint) = -2994231.4723
> >>>> Ewald error estimate: 0.6943E-04
> >>>>
> >>
> ------------------------------------------------------------------------------
> >>>>
> >>>>
> >>>> NSTEP = 797 TIME(PS) = 0.797 TEMP(K) = 286.04 PRESS
> =
> >>>> 0.0
> >>>> Etot = -2958784.2270 EKtot = 35875.5721 EPtot =
> >>>> -2994659.7991
> >>>> BOND = 23435.8580 ANGLE = 2718.9276 DIHED =
> >>>> 4448.9569
> >>>> 1-4 NB = 1265.2528 1-4 EEL = 14927.2921 VDWAALS =
> >>>> 20954.0672
> >>>> EELEC = -192037.1185 EHBOND = 0.0000 RESTRAINT =
> >>>> 62.1595
> >>>> EXTERNESCF= -2870435.1946
> >>>> EAMBER (non-restraint) = -2994721.9586
> >>>> Ewald error estimate: 0.5550E-04
> >>>>
> >>
> ------------------------------------------------------------------------------
> >>>>
> >>>> vlimit exceeded for step 797; vmax = 223.1064
> >>>>
> >>>> NSTEP = 798 TIME(PS) = 0.798 TEMP(K) = 692.97 PRESS
> =
> >>>> 0.0
> >>>> Etot = -2907774.1888 EKtot = 86911.7535 EPtot =
> >>>> -2994685.9423
> >>>> BOND = 23514.7837 ANGLE = 2718.7990 DIHED =
> >>>> 4450.6613
> >>>> 1-4 NB = 1265.9952 1-4 EEL = 14925.6770 VDWAALS =
> >>>> 20952.9524
> >>>> EELEC = -192104.7780 EHBOND = 0.0000 RESTRAINT =
> >>>> 62.3920
> >>>> EXTERNESCF= -2870472.4249
> >>>> EAMBER (non-restraint) = -2994748.3344
> >>>> Ewald error estimate: 0.6306E-04
> >>>>
> >>
> ------------------------------------------------------------------------------
> >>>>
> >>>> *vlimit exceeded for step 798; vmax = ***********
> >>>>
> >>>> NSTEP = 799 TIME(PS) = 0.799 TEMP(K) = 9298.03 PRESS
> =
> >>>> 0.0
> >>>> Etot = -1820708.4883 EKtot = 1166155.2961 EPtot =
> >>>> -2986863.7844
> >>>> BOND = 29386.9020 ANGLE = 3033.3225 DIHED =
> >>>> 4524.6387
> >>>> 1-4 NB = 1281.3174 1-4 EEL = 14909.3089 VDWAALS =
> >>>> 22456.8078
> >>>> EELEC = -192281.1708 EHBOND = 0.0000 RESTRAINT =
> >>>> 73.8498
> >>>> EXTERNESCF= -2870248.7608
> >>>> EAMBER (non-restraint) = -2986937.6342
> >>>> Ewald error estimate: 0.7918E-04
> >>>>
> >>
> ------------------------------------------------------------------------------
> >>>> ...
> >>>> ...
> >>>> ...
> >>>>
> >>
> ------------------------------------------------------------------------------
> >>>>
> >>>> vlimit exceeded for step 837; vmax = **********
> >>>>
> >>>> NSTEP = 838 TIME(PS) = 0.838 TEMP(K) = 48220.98 PRESS
> =
> >>>> 0.0
> >>>> Etot = ************** EKtot = 6047856.4596 EPtot =
> >>>> **************
> >>>> BOND = 14241797.7566 ANGLE = 271885.7319 DIHED =
> >>>> 13378.3660
> >>>> 1-4 NB = ************** 1-4 EEL = 12495.8527 VDWAALS =
> >>>> **************
> >>>> EELEC = -184401.7970 EHBOND = 0.0000 RESTRAINT =
> >>>> 28859.2744
> >>>> EXTERNESCF= -2789848.0401
> >>>> EAMBER (non-restraint) = **************
> >>>> Ewald error estimate: 0.5005E-04
> >>>>
> >>
> ------------------------------------------------------------------------------
> >>>>
> =======================================================================
> >>>>
> >>>>
> >>>>
> >>>> *Gaussian error:*
> >>>>
> ========================================================================
> >>>> Leave Link 101 at Tue Mar 26 08:37:13 2019, MaxMem=10737418240 cpu:
> >>>> 13.4
> >>>> (Enter /scf-data/apps/gaussian/g09/l103.exe)
> >>>>
> >>>>
> >> GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
> >>>> Berny optimization.
> >>>> Initialization pass.
> >>>> Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07
> >>>> Number of steps in this run= 2 maximum allowed number of steps=
> >>>> 2.
> >>>>
> >> GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
> >>>>
> >>>> Leave Link 103 at Tue Mar 26 08:37:13 2019, MaxMem=10737418240 cpu:
> >>>> 0.5
> >>>> (Enter /scf-data/apps/gaussian/g09/l202.exe)
> >>>> Small interatomic distances encountered:
> >>>> 18 4 4.38D-01
> >>>> Atoms too close.
> >>>> Error termination via Lnk1e in /scf-data/apps/gaussian/g09/l202.exe
> >> at Tue
> >>>> Mar 26 08:37:14 2019.
> >>>> Job cpu time: 0 days 0 hours 0 minutes 18.3 seconds.
> >>>> File lengths (MBytes): RWF= 22 Int= 0 D2E= 0 Chk=
> >> 86
> >>>> Scr= 2
> >>>> ======================================================================
> >>>>
> >>>>
> >>>> *My input file is:*
> >>>>
> >>>>
> >>
> *=========================================================================*
> >>>> 300K constant temp QMMMMD
> >>>> &cntrl
> >>>> imin=0,
> >>>> ntb=1,
> >>>> cut=10.0,
> >>>> ntc=1, ntf=1,
> >>>> tempi=300.0, temp0=300.0,
> >>>> ntt=3, gamma_ln=1.0,
> >>>> nstlim=1000, dt=0.001,
> >>>> ntpr=1, ntwx=1,ifqnt=1,
> >>>> ntr=1,
> >>>> restraintmask=':1-22', restraint_wt=5.0,
> >>>> /
> >>>> &qmmm
> >>>>
> >>>>
> >>
> iqmatoms=5633,5634,5635,5636,5637,5638,5639,5640,5641,5642,5643,5644,5645,5646,5647,5648,5632,5687,5688,5689,5690,5691,5692,432,433,434,435,436,437,438,439,440,441,5693,5694,5695,5696,5697,5698,5699,5700,5701,5702,5703,5704,5099,5100,5101,5102,5103,5104,5105,5106,5107,5108,5109,5110,5676,5714,5715,5716,1663,1664,1665,1666,1678,1679,1680,1681,1682,1683,1698,1699,1700,1701,1702,1703,1704,1705,1706,1707,1708,1709,1710,1721,1722,1723,1724,1725,1726,1727,
> >>>> qmcharge=0,
> >>>> qmshake=0,
> >>>> qm_ewald=0, qm_pme=1,
> >>>> qm_theory='EXTERN',
> >>>> qmcut=10,
> >>>> spin=1,
> >>>> /
> >>>> &gau
> >>>> mem = '80GB',
> >>>> method = 'B3LYP',
> >>>> basis = '6-31++G(d,p)',
> >>>> num_threads = 32,
> >>>> use_template = 0,
> >>>> /
> >>>>
> >>>>
> >>
> *=========================================================================*
> >>>> _______________________________________________
> >>>> 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
> >>>
> >> _______________________________________________
> >> AMBER mailing list
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> >>
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>
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Received on Tue Mar 26 2019 - 19:30:02 PDT
