Yes, Marius! You are right, no potassium in source... I didn't know that atoms are mentioned in source.
For future readers: in gmx-cpmd source mentioned only: M (dummy Tip4p), N,C,O,H,P,S,Fe. It's quite obvious to add your own atom. Thank's a lot for help,Andrey On Jan 21, 2008 11:33 AM, Marius Retegan <[EMAIL PROTECTED]> wrote: > I remembered this morning that I had the same problem with zinc. Search > for the qm_cpmd.c file in the gromacs/src/mdlib/. Scroll down to line 308. > You will have to add potassium to that list, recompile and try again. > It should work. > Marius Retegan > > > > On Jan 21, 2008 8:53 AM, Andrey V Golovin <[EMAIL PROTECTED]> > wrote: > > > 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 <[EMAIL PROTECTED]> 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 <[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 > > > > > > > > > > ------------------------------------------------------------------------------------------------ > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: > > > http://www.gromacs.org/pipermail/gmx-users/attachments/20080119/30cf38cd/attachment.html > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > 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! > > > > > > > > End of gmx-users Digest, Vol 45, Issue 77 > > > > ***************************************** > > > > > > -- > > > Gerrit Groenhof > > > MPI biophysical chemistry > > > Goettingen > > > Germany > > > > > > _______________________________________________ > > > 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 > > ------------------------------------------------------------------------------------------------ > > > > > > _______________________________________________ > > 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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