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,
>> /
>>
>> *=========================================================================*
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Received on Tue Mar 26 2019 - 04:00:02 PDT
