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 - 03:00:02 PDT
