Sorry for not waiting a response, but I have tested with a minimization and
got the following problem:
Here is the input file:
Minimize
&cntrl
imin=1,
ntx=1,
irest=0,
maxcyc=2000,
ncyc=1000,
ntpr=100,
ntwx=0,
cut=9999.0,
ifqnt=1, nmropt = 0,
/
&qmmm
qmmask=':78&!.C,CA,HA,O,N,H|:1&!.C,O|:240,241|:239.O4',
qmcharge=1,
dftb_3rd_order = 'PA',
printcharges = 1,
qm_theory='EXTERN',
spin = 3
qmshake=1,
qm_ewald=0, qm_pme=0
qmcut=9999.0
writepdb = 1
&gau
method = 'BLYP',
basis = '6-31G*',
num_threads = 2,
mem='8GB',
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting box info from netcdf restart file
| NetCDF restart box info found
|Largest sphere to fit in unit cell has radius = 33.962
| New format PARM file being parsed.
| Version = 1.000 Date = 07/12/16 Time = 18:11:28
NATOM = 33972 NTYPES = 21 NBONH = 32107 MBONA = 1921
NTHETH = 3978 MTHETA = 2663 NPHIH = 8257 MPHIA = 8380
NHPARM = 0 NPARM = 0 NNB = 60587 NRES = 10368
NBONA = 1921 NTHETA = 2663 NPHIA = 8380 NUMBND = 85
NUMANG = 197 NPTRA = 217 NATYP = 46 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
SANDER BOMB in subroutine setup_grids
Resulting cutoff is too small for your lower limit
2016-08-04 16:29 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
> Hello Andreas. Thank you for the reply. So, setting ntb = 0 and a qmcut =
> 999 for example would be fine? Also, I was using iwrap in my MD
> simulations, and so, can I use the restart file produced at the end of the
> MD or do I need to generate another one with cpptraj and reimage it?
> Thank you
> Fabrício
>
> 2016-08-04 16:17 GMT-03:00 Dr. Andreas W. Goetz <agoetz.sdsc.edu>:
>
>> Dear Fabricio,
>>
>> Regarding triplet states: sqm (the semiempirical QM and DFTB
>> implementation in Amber) at present can only handle closed shell systems.
>> For open-shell systems you would need to use an external QM program,
>> irrespective of the QM model that you plan to use.
>>
>> Let me clarify QM/MM with external QM programs and PBC: PME is used for
>> all MM particles but not for any electrostatic interactions with the QM
>> region. Thus, if you use electronic embedding (which is default), only MM
>> charges within the cutoff (qmcut) are included in the QM Hamiltonian. The
>> QM region does not interact with particles beyond that cutoff. MM particles
>> beyond this cutoff will see a vacuum bubble instead of QM atoms. This means
>> that the electric field experienced by the QM region due its surrounding
>> changes abruptly whenever MM particles enter/leave the cutoff region.
>> Equivalent for MM particles entering/leaving the QM cutoff, leading to
>> discontinuities in the energy surface.
>>
>> The problem is less pronounced if you increase the QM/MM cutoff (qmcut).
>> While it is not ideal, you are probably fine if you use a sufficiently
>> large cutoff and thermostat.
>>
>> If you use a non-periodic system with solvent shell and cutoff (MM and
>> QM/MM) that is larger than your system, then all electrostatic interactions
>> are included and there are no discontinuities. Amber employs a soft
>> half-harmonic potential at the boundary to avoid solvent evaporation (no
>> hard wall) so energy is conserved. There is a limit to the pair list size
>> in sander, which prevents such calculations for larger systems. One thing
>> to note is that the computational cost for the MM portion of the
>> calculation can become significant for very large systems in combination
>> with a small QM region and/or fast QM method/implementation.
>>
>> All the best,
>> Andy
>>
>> —
>> Dr. Andreas W. Goetz
>> Assistant Project Scientist
>> San Diego Supercomputer Center
>> Tel: +1-858-822-4771
>> Email: agoetz.sdsc.edu
>> Web: www.awgoetz.de
>>
>> > On Aug 4, 2016, at 10:59 AM, Fabrício Bracht <fabracht1.gmail.com>
>> wrote:
>> >
>> > Hello. I have a few doubts regarding the use of Gaussian to perform
>> qm/mm.
>> > First let say that the choice of using an external qm involves the fact
>> the
>> > the catalytic group is a copper complex in the triplet state, and thus,
>> I
>> > am not sure whether semi-empirical methods would give good reliable
>> > results. But any comment on this would be appreciated.
>> > My question may be a silly one, but it is regarding the use of periodic
>> > conditions or not and the use of the large cutoff. I have performed
>> QM/MM
>> > simulations before but never considered the use of non periodic systems.
>> > The amber 16 manual states that PBC are supported with extQM but that
>> PME
>> > is not and the use of the cutoff leads to discontinuities in the energy
>> > surface. So the manual advises you to use non-periodic simulations.
>> Well,
>> > I do not understand why that is a better choice. From what I understood,
>> > the use of a non periodic system means that there is no imaging and
>> thus,
>> > every molecule that hits the border interacts with the border. Wouldn't
>> > this affect the energy conservation more than the discontinuity caused
>> by
>> > the large cutoff in a periodic system?
>> > Do you have any recommendation as to how to setup the system. A have the
>> > structure from a very long classic MD simulation solvated in a cubic
>> box.
>> > Thank you
>> > Fabrício Bracht
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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>>
>
>
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Received on Thu Aug 04 2016 - 13:30:02 PDT
