Hi,
A few suggestions here:
- Run QM/MM minimization before you start QM/MM MD (heating)
- Do heating more carefully, with at least dt=0.001 and perhaps dt=0.0005.
- Do you need your restraints in the QM/MM heating phase? I would advise
first try to heat and then equilibrate the QM/MM system without restraints
before you model the reaction.
- Perhaps run all your QM/MM MD with dt=0.001 (in which case you could turn
of shake for the MM region as well)
And, throughout, carefully check your geometries - your QM region is large,
and you don't know if it is well described by the QM and MM combination
chosen. Do you know if the QM method you use describes your QM system /
substrate well (e.g. by comparison to higher level QM methods)?
Good luck!
--Marc
On 13 February 2012 05:08, tonghf <tonghf.zju.edu.cn> wrote:
> I use Amber QM/MM to simulate the enzyme catalysis, the catalytic process
> involves the bond broken and formation, so for the QM part, I did not use
> qmshake.
>
> First,
> I simulate the enzyme-ligand system using the traditional MM method, then
> taking the complex structure from the MM simulation as the initial
> structure,
> QM/MM was run. I first run the MM energy minimization, then carried out the
> heating progress,
>
> heating
>
> &cntrl
>
>
> imin=0,irest=0,ntx=1,
>
>
> nstlim=25000,dt=0.002,
>
>
> ntc=2,ntf=2,pencut=-0.001,
>
>
> cut=10.0, ntb=1,
>
>
> ntpr=500, ntwx=500,
>
>
> ntt=3, gamma_ln=2.0,
>
>
> tempi=0.0, temp0=300.0,
>
>
> nmropt=1,
>
>
> ifqnt=1
>
> /
>
> &qmmm
>
>
>
> iqmatoms=2058,2059,2060,2061,2062,2471,2472,2473,2474,2475,2476,2477,2468,2469,2470,2907,2908,2909,2910,2911,2912,
>
>
>
>
> 3317,3318,3319,3320,3321,3322,2432,2433,2434,2435,2436,2437,2438,2439,2440,2441,4790,4791,4792,4793,
>
>
>
>
> 4794,4795,4796,5475,5476,5477,3730,3731,3732,3733,3734,3735,4474,4475,4476,4477,4478,4479,4480,4481,4482,
>
>
>
>
> 5452,5453,5454,5455,5456,5457,5458,5459,5460,5461,5462,5463,5464,5465,5466,5467,5468,5469,
>
>
> qmcharge=0,
>
>
> qmshake=0,
>
>
> qm_ewald=1, qm_pme=1
>
> /
>
> &wt TYPE='TEMP0', istep1=0, istep2=25000,
>
>
> value1=0.1, value2=300.0, /
>
> &wt type='REST',
> istep1=0,istep2=5000,value1=0.1,
>
>
>
> value2=1.0,
>
> /
>
>
> &wt type='REST',
> istep1=5001,istep2=25000,value1=1.0,
>
>
>
> value2=1.0,
>
> /
>
> &wt TYPE='END' /
>
> LISTOUT=POUT
>
>
>
> DISANG=RST.wc
> After 2500 steps, the following error occurred:
> QMMM: WARNING!
> QMMM: Unable to achieve self consistency to
> the tolerances specified
> QMMM: No convergence in SCF after
>
> 1000 steps.
> QMMM: Job will continue with unconverged
> SCF. Warning energies
> QMMM: and forces for this step will not be
> accurate.
> QMMM: E =
>
> -0.2065E+07 DeltaE =
>
> 0.2495E+02 DeltaP =
>
> 0.8346E-01
> QMMM: Smallest
> DeltaE =
>
> 0.8698E+00 DeltaP =
>
> 0.1194E-01 Step =
>
> 96
>
> QMMM: WARNING!
> QMMM: Unable to achieve self consistency to
> the tolerances specified
> QMMM: No convergence in SCF after
>
> 1000 steps.
> QMMM: Job will continue with unconverged
> SCF. Warning energies
> QMMM: and forces for this step will not be
> accurate.
> QMMM: E =
>
> -0.2066E+07 DeltaE =
>
> 0.4190E+01 DeltaP =
>
> 0.6703E-01
> QMMM: Smallest
> DeltaE =
>
> 0.5521E+00 DeltaP =
>
> 0.5861E-01 Step =
>
> 56
>
> QMMM: WARNING!
> QMMM: Unable to achieve self consistency to
> the tolerances specified
> QMMM: No convergence in SCF after
>
> 1000 steps.
> QMMM: Job will continue with unconverged
> SCF. Warning energies
> QMMM: and forces for this step will not be
> accurate.
> QMMM: E =
>
> -0.2067E+07 DeltaE =
>
> 0.1638E+02 DeltaP =
>
> 0.3070E-01
> QMMM: Smallest
> DeltaE =
>
> -0.1253E-04 DeltaP =
>
> 0.5759E-07 Step =
>
> 77
>
> QMMM: WARNING!
> QMMM: Unable to achieve self consistency to
> the tolerances specified
> QMMM: No convergence in SCF after
>
> 1000 steps.
> QMMM: Job will continue with unconverged
> SCF. Warning energies
> QMMM: and forces for this step will not be
> accurate.
> QMMM: E =
>
> -0.2067E+07 DeltaE =
>
> -0.5213E+02 DeltaP =
>
> 0.9210E-01
> QMMM: Smallest
> DeltaE =
>
> 0.1905E-02 DeltaP =
>
> 0.2358E-01 Step =
>
> 457
>
> vlimit exceeded for step
>
> 2509; vmax =
>
> 21.0047
> vlimit exceeded for step
>
> 2510; vmax =
>
> 49.6459
> vlimit exceeded for step
>
> 2511; vmax =
>
> 45.8189
>
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
>
>
> deviation is too large
>
>
> NITER, NIT, LL, I and J are :
>
>
> 0
>
> 3
>
> 2245
>
>
> 4494
>
> 4497
>
>
> Note: This is usually a symptom of some deeper
>
>
> problem with the energetics of the system.
> Therefore, how can I solve the problem?
> How should I do to relax the QM part of the
> system?
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 13 2012 - 01:30:02 PST
