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
> 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 Tue Mar 26 2019 - 07:00:03 PDT
