[CP2K:1903] Re: methane in a water box QM/MM

[Marius Retegan]

Hello again,

I was a little hasty with my previous email, since some things are a little
unclear.
I looked at the PERIODIC section in QMMM but sincerely that was of very
little help.
So if I want to do periodic QMMM, I should remove the decoupling from the QM
part and add CELL information in the QMMM part. Additionally in the QMMM
part I should also add PERIODIC. If this is correct, I'm stuck since I don't
know what parameters to chose next.

Usually, I'm not used to asking so many questions regarding the softwares
that I used, since I try as much as possible to find the answer alone. With
cp2k (especially the QM/MM part) this is very difficult, mostly due to the
its particular nature (plainwaves, original techniques for computing QM/MM
electrostatic potential, etc...).
I saw many times being said on the list, that the test are hardly something
to take as viable production runs, since they are made for speed. The manual
is OK for constructing your input, but it provides very little help in
choosing the "right" parameters for your system. I understand that
parameters depend on the system studied, but some heads-up on what is safe
to use would be nice. What happend with the wiki based documentation
proposal? I think that having a great software is important, but giving new
users a place to start is equally important.

Please don't take this email as hostility towards cp2k (very far from my
intentions), but more as lines coming from a "frustrated" user who tries to
see the light at the end of the tunnel :).

Thanks
Marius

On Wed, Mar 18, 2009 at 5:18 PM, Marius Retegan
<marius.s... at gmail.com>wrote:

> Thanks a lot for all your comments.
>
> Marius
>
>
> On Wed, Mar 18, 2009 at 5:14 PM, Teodoro Laino <teodor... at gmail.com>wrote:
>
>>
>> The bug (which was depending on the way of reading natively AMBER prmtop
>> files) is now fixed in the CVS (thanks for reporting)!
>> Just few comments about your QMMM setup.
>> 1) The way it is setup you will hardly have a conserved energy (you have
>> a PERIODIC MM) but you don't use the periodic QMMM version (see PERIODIC
>> in QMMM). Alternatively you may think about using a spherical cutoff for
>> the electrostatic (that is tapering the interaction after a certain
>> cutoff).
>> 2) you may want to specify proper covalent radius for the QMMM
>> electrostatic interactions (at the moment you rely on the default which
>> is 0.78 (if I'm not wrong) for all atoms).
>>
>> Have a nice QMMM.
>> Teo
>>
>> p.s.: about the xc_deriv and xc_smooth_rho I would not suggest you to
>> use them unless you really know what you are doing. Most of the time you
>> don't need to specify those keywords (only for few pathological cases.
>> CH4 or H2O are definitely not one of them).
>>
>>
>> Marius Retegan wrote:
>> > Hi,
>> >
>> > In my continuing saga of using cp2k for running qm/mm calculations I
>> > have encounter yet another bump.
>> > While using the input below I get this error "FORCEFIELD| Missing Bond
>> >              (  CT,  HC)" and angle ...
>> >
>> > &GLOBAL
>> >   PROJECT mebox_qmmm
>> >   RUN_TYPE MD
>> >   PRINT_LEVEL LOW
>> > &END GLOBAL
>> >
>> > &MOTION
>> >   &MD
>> >    ENSEMBLE NVT
>> >    STEPS 1000
>> >    TIMESTEP 1.0
>> >    TEMPERATURE 298
>> >    &THERMOSTAT
>> >      REGION GLOBAL
>> >      TYPE CSVR
>> >      &CSVR
>> >        TIMECON 100
>> >      &END CSVR
>> >    &END THERMOSTAT
>> >   &END MD
>> >   &PRINT
>> >     &RESTART OFF
>> >     &END RESTART
>> >     &RESTART_HISTORY OFF
>> >     &END RESTART_HISTORY
>> >   &END PRINT
>> > &END MOTION
>> >
>> > &FORCE_EVAL
>> >   METHOD QMMM
>> >
>> >   &DFT
>> >     CHARGE 0
>> >     BASIS_SET_FILE_NAME         GTH_BASIS_SETS
>> >     POTENTIAL_FILE_NAME         GTH_POTENTIALS
>> >     &MGRID
>> >       CUTOFF 280
>> >       COMMENSURATE
>> >     &END MGRID
>> >     &SCF
>> >       MAX_SCF     20
>> >       EPS_SCF     1.0E-6
>> >       &OT T
>> >         PRECONDITIONER FULL_ALL
>> >         MINIMIZER DIIS
>> >       &END OT
>> >       &PRINT
>> >         &RESTART OFF
>> >         &END RESTART
>> >         &RESTART_HISTORY OFF
>> >         &END RESTART_HISTORY
>> >       &END PRINT
>> >     &END SCF
>> >     &QS
>> >       EPS_DEFAULT 1.0E-12
>> >       MAP_CONSISTENT
>> >       EXTRAPOLATION ASPC
>> >       EXTRAPOLATION_ORDER 3
>> >     &END QS
>> >     &XC
>> >       &XC_GRID
>> >         XC_SMOOTH_RHO NN10
>> >         XC_DERIV NN10_SMOOTH
>> >       &END XC_GRID
>> >       &XC_FUNCTIONAL BLYP
>> >       &END XC_FUNCTIONAL
>> >     &END XC
>> >     &POISSON
>> >       POISSON_SOLVER MULTIPOLE
>> >       PERIODIC NONE
>> >     &END POISSON
>> >   &END DFT
>> >
>> >   &MM
>> >     &FORCEFIELD
>> >       VDW_SCALE14 0.5
>> >       EI_SCALE14  0.8333333
>> >       SCALE_CUTOFF .FALSE.
>> >       PARM_FILE_NAME mebox.prmtop
>> >       PARMTYPE AMBER
>> >       &SPLINE
>> >         EMAX_SPLINE 1.0
>> >         RCUT_NB 10
>> >       &END
>> >     &END FORCEFIELD
>> >     &POISSON
>> >       &EWALD
>> >         EWALD_TYPE SPME
>> >         ALPHA .36
>> >         GMAX 23 23 23
>> >       &END EWALD
>> >     &END POISSON
>> >   &END MM
>> >
>> >   &QMMM
>> >     E_COUPL GAUSS
>> >     USE_GEEP_LIB  7
>> >     &CELL
>> >       ABC 8.0 8.0 8.0
>> >       PERIODIC NONE
>> >     &END CELL
>> >     &QM_KIND C
>> >       MM_INDEX 1
>> >     &END QM_KIND
>> >     &QM_KIND H
>> >       MM_INDEX 2 3 4 5
>> >     &END QM_KIND
>> >   &END QMMM
>> >
>> >   &SUBSYS
>> >     &CELL
>> >       ABC [angstrom] 23.2782522  22.7141099  23.2326917
>> >       PERIODIC XYZ
>> >     &END CELL
>> >     &TOPOLOGY
>> >       COORDINATE PDB
>> >       COORD_FILE_NAME mebox_npt.pdb
>> >       CONNECTIVITY AMBER
>> >       CONN_FILE_NAME mebox.prmtop
>> >     &END
>> >     &KIND C
>> >       BASIS_SET DZVP-GTH
>> >       POTENTIAL GTH-BLYP-q4
>> >     &END KIND
>> >     &KIND H
>> >       BASIS_SET DZVP-GTH
>> >       POTENTIAL GTH-BLYP-q1
>> >     &END KIND
>> >   &END SUBSYS
>> > &END FORCE_EVAL
>> >
>> > If I change QMMM with FIST the input runs.
>> >
>> > I also have some additional questions, but on somewhat different
>> matters.
>> >
>> > In the latest papers that I could find that use cp2k to do qm/mm
>> > calculations (http://dx.doi.org/10.1021/ja076081h and
>> > http://dx.doi.org/10.1021/jp074858n) the authors used a integration
>> > step of 0.5 and 0.48. Unfortunately, they did not discussed their
>> > choice. I'm used to running qm/mm md with other packages, but I've
>> > always used an integration step of 1 fs. Is cp2k different :-)?
>> >
>> > Is there any place where I can find information regarding the
>> > parameters xc_deriv and xc_smooth_rho and are "good" choices?
>> >
>> > Thanks,
>> > Marius
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > >
>>
>>
>> >>
>>
>
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