[gmx-users] GMX CPMD K+ ion problem

[Andrey V Golovin]

Dear Marius,
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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