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

Andrey V Golovin golovin at belozersky.msu.ru
Mon Jan 21 08:53:02 CET 2008 

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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> >>
> >>
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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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