methane in a water box QM/MM

[Axel]

On Mar 18, 2:29 pm, Marius Retegan <marius.s... at gmail.com> wrote:

> 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

marius,

if you can demonstrate that you made a reasonable effort to
find out things on your own, nobody is going to going to complain,
and most are happy to help. the irritating questions are questions
that say something along the lines of "can somebody give me a step-by-
step
documentation for how to do <insert-a-horribly-complicated-method-
here>
and by the way i have never ever used cp2k before, so please explain
everything to me.

> 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...).

it _is_ difficult. the only way to make it easy is to hide all the
details from you and have the software use hardcoded defaults. even
though it is tough at the beginning, there is some advantage to having
to fight your way through it, you get a much deeper understanding of
what is going on and can use cp2k much better afterwards. if you look
at very old messages in this forum, you can find some similarly
frustrated
messages written by me as well.

> 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.

yes, but who is in the best position to do this?
the person who is currently struggling with it, i.e. you!

there are always a lot of good ideas and sometimes even people
get started, but it is difficult to keep the momentum, particularly
if there is nobody else stepping up to get involved, too.
i can give you an example from my personal experience.
a lot of what was done in the last few years in updating the
manual of the CPMD package and the related tutorials were written
while i was learning how to use and program CPMD myself. now
that i've also contributed a few features, i learned that if you
program something for your own needs, or to help somebody you
are working with, you rarely have the energy left to document
everything so that a beginner can deal with it, because for
yourself it is all very obvious. but if you are trying to learn
it yourself, it can be even helpful to write down what you understood
and have more experienced people point out your mistakes to you.

every problem is also an opportunity.

cheers,
    axel.

> 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/ja076081hand
> >> >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