Yes, Marius!<br>You are right, no potassium in source... I didn't know that atoms are mentioned in source. <br><br>For future readers: in gmx-cpmd source mentioned only: M (dummy Tip4p), N,C,O,H,P,S,Fe.<br>It's quite obvious to add your own atom.
<br><br>Thank's a lot for help,Andrey<br><br><div class="gmail_quote">On Jan 21, 2008 11:33 AM, 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;">
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.<br>
It should work.
<br><font color="#888888">Marius Retegan</font><div><div></div><div class="Wj3C7c"><br><br><br><div class="gmail_quote">On Jan 21, 2008 8:53 AM, Andrey V Golovin <<a href="mailto:golovin@belozersky.msu.ru" target="_blank">
golovin@belozersky.msu.ru</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;">
Gerrit,<br>here is my output:<div><br>QM/MM calculation requested.<br>Layer 0<br></div>nr of QM atoms 9<br><br>... exactly that really confusing me, looks like gromacs says 9 atoms but at some level K is just ignored.
<div><div></div><div><br><br><br><br>
<div class="gmail_quote">On Jan 19, 2008 9:49 PM, ggroenh <<a href="mailto:ggroenh@gwdg.de" target="_blank">ggroenh@gwdg.de</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;">
><br><br>Before step 1, gromacs outputs the number of atoms per QM layer, e.g.<br><br>Reading file topol.tpr, VERSION 3.3_rc3 (single precision)<br>QM/MM calculation requested.<br>Layer 0<br>nr of QM atoms 20<br>QMlevel: CASSCF/3-21G,CASelectrons=6,CASorbitals=6
<br><br><br>How much are there in your simulaiton? This might tell if it goes<br>wrong in gromacs side, or in cpmd.<br><br>Gerrit<br><div><div></div><div><br><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>> On Jan 18, 2008 7:23 PM, Marius Retegan <<a href="mailto:marius.s.retegan@gmail.com" target="_blank">marius.s.retegan@gmail.com</a>><br>> wrote:<br>><br>>> For the Gromacs-CPMD interface you have to specify the QM groups in
<br>>> your<br>>> .mdp file like this "QMMM-grps = QM_part". Then open<br>>> your<br>>> index file and create an atom group with the same name "QM_part"<br>>> and add in
<br>>> 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<br>>> calculation.<br>>> Marius Retegan<br>>><br>>><br>
>> On Jan 18, 2008 12:25 PM, Andrey V Golovin <
<a href="mailto:golovin@belozersky.msu.ru" target="_blank">golovin@belozersky.msu.ru</a><br>>> ><br>>> wrote:<br>>><br>>>> Dear all,<br>>>> We successfully passed all examples in GMX-CPMD and some other stuff
<br>>>> with amberff with common atoms, but since we trying to deal with K+<br>>>> (potassium) in QM part, we see every time absence of potassium in<br>>>> CPMD_inp.run, it's just skipped. In very beginning CPMD shows
<br>>>> right number<br>>>> 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
<br>>>> amber_XX or<br>>>> 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>>>><br>>>> --<br>>>> Best regards, Andrey<br>>>> ------------------------------------------------------------------------------------------------
<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" 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><br>>>> ------------------------------------------------------------------------------------------------<br>>>><br>>>><br>>>><br>>>><br>>>>
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<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:
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<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
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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
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