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 <[EMAIL PROTECTED]>
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 < [EMAIL PROTECTED]
>
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: [EMAIL PROTECTED]
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: [EMAIL PROTECTED]
Russia web: http://rnp-group.genebee.msu.su
------------------------------------------------------------------------------------------------
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Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
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