[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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