Dear Marius,<br>We pointed qm group in index .<br>,,,,,,,,,,,,,,,,,,,,,,,,,,,<br>[ QM ]<br> 17 50 147 180 310 343 440 473 489<br>...........................<br>and mdp,<br>............<br>; OPTIONS FOR QMMM calculations
<br>QMMM = yes<br>; Groups treated Quantum Mechanically<br>QMMM-grps = QM<br>; QM method <br>QMmethod = CPMD<br>; QMMM scheme <br>QMMMscheme = normal
<br>; QM basisset <br>QMbasis = STO-3G<br>; QM charge <br>QMcharge = 1<br>.........<br><br>CPMD_inp.tmpl:<br>.......<br>&ATOMS<br>*O_VDB_BLYP.psp FORMATTED<br>LMAX=P
<br>*K_VDB_BLYP.psp FORMATTED<br>LMAX=P LOCAL=S<br>.......<br><br>All these gives such CPMD_inp.run<br>.............<br>&ATOMS<br>*O_VDB_BLYP.psp FORMATTED<br>LMAX=P<br> 8<br> 14.8440376 8.2394453 13.9464178<br>
10.7622295 7.4646576 9.5055617<br> 7.7575652 10.3370411 13.7574452<br> 11.9716541 12.9448630 16.9321848<br> 12.6519555 17.0644656 12.7936849<br> 8.1544076 15.0802534 10.3559384<br> 12.5952637
12.5102260 6.8410481<br> 17.0739143 12.9448630 9.8079179<br>&END<br>..............<br><br>Potassium (9th atom) just skipped.<br>Any clue?<br><br><br><br><div class="gmail_quote">On Jan 18, 2008 7:23 PM, Marius Retegan <
<a href="mailto:marius.s.retegan@gmail.com">marius.s.retegan@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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.
<br>If this doesn't work you should send to the list a output of you calculation.<br>Marius Retegan<br><br><br><div class="gmail_quote"><div><div></div><div class="Wj3C7c">On Jan 18, 2008 12:25 PM, Andrey V Golovin <
<a href="mailto:golovin@belozersky.msu.ru" target="_blank">
golovin@belozersky.msu.ru</a>> wrote:<br></div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="Wj3C7c">
Dear all,<br><div class="gmail_quote">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.
<br><br>Potassium and pseudopotential was included in CPMD_inp.tmpl.<br>We checked different ways of including Potassium in ff, like amber_XX or just K+.<br>Pseudopotential was build with Ultrasoft Pseudopotential Package.
<br>Gmx-cpmd was compiled from site P. K. Biswas.<br><br>Any ideas?<br>Thanks in advance, Andrey<br clear="all"><br>-- <br>Best regards, Andrey<br><font color="#888888">------------------------------------------------------------------------------------------------
<br>Andrey V. Golovin<br>Ph.D, Assistant professor tel: +7 (495) 939-5305 <br>Bioengineering and<br>Bioinformatics Department <br>Moscow State University fax: +7 (495) 939-3181<br>119992 Moscow E-mail:
<a href="mailto:golovin@genebee.msu.su" target="_blank">golovin@genebee.msu.su</a><br>Russia web: <a href="http://rnp-group.genebee.msu.su" target="_blank">http://rnp-group.genebee.msu.su</a>
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Best regards, Andrey<br>------------------------------------------------------------------------------------------------<br>Andrey V. Golovin<br>Ph.D, Assistant professor tel: +7 (495) 939-5305
<br>Bioengineering and<br>Bioinformatics Department <br>Moscow State University fax: +7 (495) 939-3181<br>119992 Moscow E-mail: <a href="mailto:golovin@genebee.msu.su">golovin@genebee.msu.su
</a><br>Russia web: <a href="http://rnp-group.genebee.msu.su">http://rnp-group.genebee.msu.su</a><br>------------------------------------------------------------------------------------------------