[CP2K:1907] Re: methane in a water box QM/MM

Marius Retegan marius.s... at gmail.com
Thu Mar 19 08:50:49 UTC 2009


Hello,

Thank you for the help. At the moment I don't feel sufficiently comfortable
with writing a qm/mm tutorial, since I just started using cp2k. As soon as
things start to crystallize, I'm going to write a draft, that other, more
experience people, can polish. Until then it's possible that I'm going to
spam the list with other questions :-).

Marius

On Wed, Mar 18, 2009 at 8:06 PM, Teodoro Laino <teodor... at gmail.com>wrote:

>
> Hi Marius,
>
> we discussed so many time about the documentation that is almost an
> exhausted thread :-).
> Anyway.. Axel started with the pages on the google forum and they are
> exactly in the state he left them..
> Why don't you take over and contribute to them?
>
> Let's just go back now to your question..
> When you want to do a PERIODIC QMMM calculation, conceptually speaking
> you have to decouple and recouple the QM images with the proper
> periodicity.
> have a look at:
> QMMM/QS/regtest-4/crys_per_qmmm.inp, which is true that it is a regtest
> but is still ok as a starting point..
>
> First don't forget in all QMMM runs that use quickstep to add
> COMMENSURATE to the MGRID section. It is mandatory!
>
> Second if you do fully periodic QMMM you don't have to specify any
> poisson section in the DFT section (since the decoupling is handled
> directly with the re-coupling).
> In the CELL section of the QMMM section you have to enable fully
> PERIODIC (i.e. delete possible PERIODIC NONE in both cell sections) and
> add to the QMMM section the PERIODIC section:
>
>
> &PERIODIC
>  GMAX 0.5 (is a reasonable value.. but depends on the GEEP expansion ..
> USE_GEEP_LIB 10 is good enough)
>  &MULTIPOLE
>     EWALD_PRECISION 1.0E-6
>     RCUT  CELL/2 (is good enough)
>  &END
> &END
>
> at the moment the only way to decouple and recouple is with the
> MULTIPOLE scheme.
> You can start from these hints and check the set of parameters better
> for you.
> And in case you have still time and willingness put down a couple of
> pages on how to use the QMMM in cp2k.
> Future users will be extremely glad. ;-)
> Cheers
> Teo
>
> Marius Retegan wrote:
> > 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 <mailto: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 <mailto: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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