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 <[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 > > ------------------------------------------------------------------------------------------------ > > > > > > > > > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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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