[gmx-users] Re: GMX CPMD K+ ion problem

Andrey V Golovin golovin at belozersky.msu.ru
Mon Jan 21 10:28:16 CET 2008 

Yes, Marius!
You are right, no potassium in source... I didn't know that atoms are
mentioned in source.

For future readers: in gmx-cpmd source mentioned only: M (dummy Tip4p),
N,C,O,H,P,S,Fe.
It's quite obvious to add your own atom.

Thank's a lot for help,Andrey

On Jan 21, 2008 11:33 AM, Marius Retegan <marius.s.retegan at gmail.com> wrote:

> I remembered this morning that I had the same problem with zinc. Search
> for the qm_cpmd.c file in the gromacs/src/mdlib/.  Scroll down to line 308.
> You will have to add potassium to that list, recompile and try again.
> It should work.
> Marius Retegan
>
>
>
> On Jan 21, 2008 8:53 AM, Andrey V Golovin <golovin at belozersky.msu.ru>
> wrote:
>
> > Gerrit,
> > here is  my output:
> > QM/MM calculation requested.
> > Layer 0
> > nr of QM atoms 9
> >
> > ... exactly that really confusing me, looks like gromacs says 9 atoms
> > but at some level K is just ignored.
> >
> >
> >
> >
> > On Jan 19, 2008 9:49 PM, ggroenh <ggroenh at gwdg.de> wrote:
> >
> > > >
> > >
> > > Before step 1, gromacs outputs the number of atoms per QM layer, e.g.
> > >
> > > Reading file topol.tpr, VERSION 3.3_rc3 (single precision)
> > > QM/MM calculation requested.
> > > Layer 0
> > > nr of QM atoms 20
> > > QMlevel: CASSCF/3-21G,CASelectrons=6,CASorbitals=6
> > >
> > >
> > > How much are there in your simulaiton? This might tell if it goes
> > > wrong in gromacs side, or in cpmd.
> > >
> > > Gerrit
> > >
> > >
> > > > We pointed qm group in index .
> > > > ,,,,,,,,,,,,,,,,,,,,,,,,,,,
> > > > [ QM ]
> > > >  17   50  147  180  310  343  440  473 489
> > > > ...........................
> > > > and mdp,
> > > > ............
> > > > ; OPTIONS FOR QMMM calculations
> > > > QMMM                     = yes
> > > > ; Groups treated Quantum Mechanically
> > > > QMMM-grps                = QM
> > > > ; QM method
> > > > QMmethod                 = CPMD
> > > > ; QMMM scheme
> > > > QMMMscheme               = normal
> > > > ; QM basisset
> > > > QMbasis                  = STO-3G
> > > > ; QM charge
> > > > QMcharge                 = 1
> > > > .........
> > > >
> > > > CPMD_inp.tmpl:
> > > > .......
> > > > &ATOMS
> > > > *O_VDB_BLYP.psp FORMATTED
> > > > LMAX=P
> > > > *K_VDB_BLYP.psp FORMATTED
> > > > LMAX=P LOCAL=S
> > > > .......
> > > >
> > > > All these gives such CPMD_inp.run
> > > > .............
> > > > &ATOMS
> > > > *O_VDB_BLYP.psp FORMATTED
> > > > LMAX=P
> > > > 8
> > > >  14.8440376    8.2394453   13.9464178
> > > >  10.7622295    7.4646576    9.5055617
> > > >   7.7575652   10.3370411   13.7574452
> > > >  11.9716541   12.9448630   16.9321848
> > > >  12.6519555   17.0644656   12.7936849
> > > >   8.1544076   15.0802534   10.3559384
> > > >  12.5952637   12.5102260    6.8410481
> > > >  17.0739143   12.9448630    9.8079179
> > > > &END
> > > > ..............
> > > >
> > > > Potassium (9th atom) just skipped.
> > > > Any clue?
> > > >
> > > >
> > > >
> > > > On Jan 18, 2008 7:23 PM, Marius Retegan <marius.s.retegan at gmail.com>
> > > > wrote:
> > > >
> > > >> For the Gromacs-CPMD interface you have to specify the QM groups in
> > >
> > > >> your
> > > >> .mdp file like this "QMMM-grps                = QM_part". Then open
> > > >> your
> > > >> index file and create an atom group with the same name "QM_part"
> > > >> and add in
> > > >> it all atoms that you want to treat with CPMD.
> > > >> If this doesn't work you should send to the list a output of you
> > > >> calculation.
> > > >> Marius Retegan
> > > >>
> > > >>
> > > >> On Jan 18, 2008 12:25 PM, Andrey V Golovin <
> > > golovin at belozersky.msu.ru
> > > >> >
> > > >> wrote:
> > > >>
> > > >>> Dear all,
> > > >>> We successfully passed all examples in GMX-CPMD and some other
> > > stuff
> > > >>> with amberff with common atoms, but since we trying to deal with
> > > K+
> > > >>> (potassium)  in QM  part, we see every time absence of potassium
> > > in
> > > >>> CPMD_inp.run, it's just skipped. In very beginning CPMD shows
> > > >>> right number
> > > >>> of atoms in QM group, but K is not mentioned in cpmd input file.
> > > >>>
> > > >>> Potassium and pseudopotential was included in CPMD_inp.tmpl.
> > > >>> We checked different ways of including Potassium in ff, like
> > > >>> amber_XX or
> > > >>> just K+.
> > > >>> Pseudopotential was build with Ultrasoft Pseudopotential Package.
> > > >>> Gmx-cpmd was compiled from site P. K. Biswas.
> > > >>>
> > > >>> Any ideas?
> > > >>> Thanks in advance, Andrey
> > > >>>
> > > >>> --
> > > >>> Best regards, Andrey
> > > >>>
> > > ------------------------------------------------------------------------------------------------
> > >
> > > >>>
> > > >>> Andrey V. Golovin
> > > >>> Ph.D, Assistant professor   tel: +7 (495) 939-5305
> > > >>> Bioengineering and
> > > >>> Bioinformatics Department
> > > >>> Moscow State University     fax: +7 (495) 939-3181
> > > >>> 119992 Moscow                 E-mail: golovin at genebee.msu.su
> > > >>> Russia                              web:
> > > http://rnp-group.genebee.msu.su
> > > >>>
> > > ------------------------------------------------------------------------------------------------
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>> _______________________________________________
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> > > >
> > > >
> > > > --
> > > > Best regards, Andrey
> > > >
> > > ------------------------------------------------------------------------------------------------
> > >
> > > > Andrey V. Golovin
> > > > Ph.D, Assistant professor   tel: +7 (495) 939-5305
> > > > Bioengineering and
> > > > Bioinformatics Department
> > > > Moscow State University     fax: +7 (495) 939-3181
> > > > 119992 Moscow                 E-mail: golovin at genebee.msu.su
> > > > Russia                              web: http://rnp-group.genebee.msu.su
> > >
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> > >
> > > --
> > > Gerrit Groenhof
> > > MPI biophysical chemistry
> > > Goettingen
> > > Germany
> > >
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> >
> > --
> >
> > Best regards, Andrey
> > ------------------------------------------------------------------------------------------------
> >
> > Andrey V. Golovin
> > Ph.D, Assistant professor   tel: +7 (495) 939-5305
> > Bioengineering and
> > Bioinformatics Department
> > Moscow State University     fax: +7 (495) 939-3181
> > 119992 Moscow                 E-mail: golovin at genebee.msu.su
> > Russia                              web: http://rnp-group.genebee.msu.su
> > ------------------------------------------------------------------------------------------------
> >
> >
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-- 
Best regards, Andrey
------------------------------------------------------------------------------------------------
Andrey V. Golovin
Ph.D, Assistant professor   tel: +7 (495) 939-5305
Bioengineering and
Bioinformatics Department
Moscow State University     fax: +7 (495) 939-3181
119992 Moscow                 E-mail: golovin at genebee.msu.su
Russia                              web: http://rnp-group.genebee.msu.su
------------------------------------------------------------------------------------------------
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