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

[ggroenh]

>

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