<div dir="ltr">Dear Teo, Hi, <g class="gr_ gr_976 gr-alert gr_gramm gr_inline_cards gr_run_anim Grammar only-ins doubleReplace replaceWithoutSep" id="976" data-gr-id="976">kind</g> section for D does not <g class="gr_ gr_966 gr-alert gr_gramm gr_inline_cards gr_run_anim Grammar multiReplace" id="966" data-gr-id="966">seems</g> to work in QMMM setup. I am trying to set up QMMM simulation for di-peptide in D2O and also I want to deuterate certain H atoms of <g class="gr_ gr_1539 gr-alert gr_gramm gr_inline_cards gr_run_anim Grammar only-ins replaceWithoutSep" id="1539" data-gr-id="1539">dipeptide</g>. After preparing <g class="gr_ gr_1678 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling ins-del multiReplace" id="1678" data-gr-id="1678">coorinates</g> and topology file with AMBER tools, I have <g class="gr_ gr_1721 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling ins-del multiReplace" id="1721" data-gr-id="1721">modifiled</g> it with PARMED . CP2K reads the topology correctly with masses as intended for dipeptide (also D2O) in the FIST module. But in the Quickstep and QM section of QMMM _QM_ atoms which are deuterated in the MM does seem to be not deuterated. For example (copied from the output file) MODULE FIST: ATOMIC COORDINATES IN ANGSTROM Atom Kind ATM_TYP X Y Z q(eff) Mass 1 1 _QM_ 3.971530 11.274613 5.974515 0.00 14.0100 2 2 _QM_ 4.861530 11.734613 6.124515 0.00 2.0140 #deuteated 3 2 _QM_ 3.401530 12.004613 5.574515 0.00 2.0140 4 2 _QM_ 3.581530 11.074613 6.884515 0.00 2.0140 5 3 _QM_ 4.211530 10.104613 5.124515 0.00 12.0100 6 4 _QM_ 3.481530 9.344613 5.394515 0.00 1.0080 7 5 _QM_ 4.131530 10.454613 3.634515 0.00 12.0100 8 6 _QM_ 3.211530 10.964613 3.384515 0.00 1.0080 9 6 _QM_ 4.921530 11.134613 3.324515 0.00 1.0080 10 6 _QM_ 4.291530 9.514613 3.104515 0.00 1.0080 11 7 _QM_ 5.551530 9.434613 5.384515 0.00 12.0100 12 8 _QM_ 6.581530 10.014613 5.734515 0.00 16.0000 13 9 _QM_ 5.511530 8.094613 5.304515 0.00 14.0100 14 10 _QM_ 4.621530 7.744613 4.984515 0.00 2.0140 15 11 _QM_ 6.681530 7.254613 5.444515 0.00 12.0100 16 12 _QM_ 7.171530 7.674613 6.314515 0.00 1.0080 17 13 _QM_ 6.221530 5.884613 5.954515 0.00 12.0100 18 14 _QM_ 5.681530 6.034613 6.884515 0.00 1.0080 19 14 _QM_ 5.581530 5.364613 5.244515 0.00 1.0080 20 15 _QM_ 7.381530 4.954613 6.324515 0.00 12.0100 21 16 _QM_ 8.111530 5.544613 6.874515 0.00 1.0080 22 17 _QM_ 8.081530 4.224613 5.174515 0.00 12.0100 23 18 _QM_ 8.691530 4.984613 4.684515 0.00 1.0080 24 18 _QM_ 8.751530 3.474613 5.574515 0.00 1.0080 25 18 _QM_ 7.401530 3.834613 4.414515 0.00 1.0080 26 17 _QM_ 6.701530 3.804613 7.064515 0.00 12.0100 27 18 _QM_ 7.421530 3.014613 7.294515 0.00 1.0080 28 18 _QM_ 6.231530 4.094613 7.994515 0.00 1.0080 29 18 _QM_ 5.891530 3.394613 6.454515 0.00 1.0080 30 19 _QM_ 7.661530 7.274613 4.284515 0.00 12.0100 31 20 _QM_ 8.841530 7.664613 4.474515 0.00 16.0000 MODULE QM/MM first QM, then MM (0 charges): ATOMIC COORDINATES IN angstrom Atom Kind Element X Y Z Z(eff) Mass 1 1 H 1 4.861530 11.734613 6.124515 1.00 1.0079 # 4 H's were deuteraated but here it does not look like that 2 1 H 1 3.401530 12.004613 5.574515 1.00 1.0079 3 1 H 1 3.581530 11.074613 6.884515 1.00 1.0079 4 1 H 1 3.481530 9.344613 5.394515 1.00 1.0079 5 1 H 1 3.211530 10.964613 3.384515 1.00 1.0079 6 1 H 1 4.921530 11.134613 3.324515 1.00 1.0079 7 1 H 1 4.291530 9.514613 3.104515 1.00 1.0079 8 1 H 1 4.621530 7.744613 4.984515 1.00 1.0079 9 1 H 1 7.171530 7.674613 6.314515 1.00 1.0079 10 1 H 1 5.681530 6.034613 6.884515 1.00 1.0079 11 1 H 1 5.581530 5.364613 5.244515 1.00 1.0079 12 1 H 1 8.111530 5.544613 6.874515 1.00 1.0079 13 1 H 1 8.691530 4.984613 4.684515 1.00 1.0079 14 1 H 1 8.751530 3.474613 5.574515 1.00 1.0079 15 1 H 1 7.401530 3.834613 4.414515 1.00 1.0079 16 1 H 1 7.421530 3.014613 7.294515 1.00 1.0079 17 1 H 1 6.231530 4.094613 7.994515 1.00 1.0079 18 1 H 1 5.891530 3.394613 6.454515 1.00 1.0079 19 2 C 6 4.211530 10.104613 5.124515 4.00 12.0107 20 2 C 6 4.131530 10.454613 3.634515 4.00 12.0107 21 2 C 6 5.551530 9.434613 5.384515 4.00 12.0107 22 2 C 6 6.681530 7.254613 5.444515 4.00 12.0107 23 2 C 6 6.221530 5.884613 5.954515 4.00 12.0107 24 2 C 6 7.381530 4.954613 6.324515 4.00 12.0107 25 2 C 6 8.081530 4.224613 5.174515 4.00 12.0107 26 2 C 6 6.701530 3.804613 7.064515 4.00 12.0107 27 2 C 6 7.661530 7.274613 4.284515 4.00 12.0107 28 3 O 8 6.581530 10.014613 5.734515 6.00 15.9994 29 3 O 8 8.841530 7.664613 4.474515 6.00 15.9994 30 3 O 8 7.201530 6.854613 3.204515 6.00 15.9994 31 4 N 7 3.971530 11.274613 5.974515 5.00 14.0067 32 4 N 7 5.511530 8.094613 5.304515 5.00 14.0067 I have also tried to read in <g class="gr_ gr_2581 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling ins-del multiReplace" id="2581" data-gr-id="2581">coorinates</g> using &COORD section and label D for deuterated atoms (with corresponding kind section the input) but there is no change in output. As QM atoms are defined using MM indexes I was wondering does CP2K uses same mass as defined in the <g class="gr_ gr_3950 gr-alert gr_gramm gr_inline_cards gr_run_anim Style multiReplace" id="3950" data-gr-id="3950">forcefield ?</g> How I can solve this technical issue? Thanks in advance. I have attached the input and output file and basic working folder which contains all the required files to run the simulation. ------------------------------------------------------------------ CP2K version 4.1 SVN source code revision svn:17462 cp2kflags: <g class="gr_ gr_3968 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling" id="3968" data-gr-id="3968">libint</g> fftw3 <g class="gr_ gr_3969 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling" id="3969" data-gr-id="3969">libxc</g> elpa3 parallel mpi3 <g class="gr_ gr_3967 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling ins-del multiReplace" id="3967" data-gr-id="3967">scalapack</g> ------------------------------------------------------------------ Best, Irtaza On Friday, November 28, 2008 at 9:45:54 PM UTC+1, Teo wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">here's the way to fix this problem: &KI ND D BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q1 MASS 2.0 ELEMENT H &END KIND teo On 28 Nov 2008, at 21:43, Eric Shamay wrote: > > Here's the error I receive when trying the following: > > *** Unknown element for KIND <D>. This problem can be fixed > specifying *** > *** properly elements in PDB or specifying a KIND section or getting > in *** > *** touch with one of the > developers! *** > > > My KIND section is as follows: > > &KIND H > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q1 > &END KIND > &KIND D > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q1 > MASS 2.0 > &END KIND > &KIND O > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q6 > &END KIND > &KIND N > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q5 > &END KIND > > > It's the error I received when trying that out before, but forgot what > the problem was. Any insight on this? > > ~Eric > > > > On Nov 21, 2:52 pm, Laino Teodoro <<a>teodor...@gmail.com</a>> wrote: >> Ciao Erick, >> >> sure it is possible. Please, follow this pseudo-input.. >> >> &COORD >> D x y z >> D x y z >> O x y z >> H x y z >> H x y z >> O x y z >> &END >> >> &KIND H >> BASIS_SET .. >> POTENTIAL .. >> &END >> >> &KIND D >> BASIS_SET .. >> POTENTIAL .. >> MASS 2.0 >> &END >> >> ...etc.. >> >> ciao, >> Teo >> >> On 21 Nov 2008, at 23:46, Eric Shamay wrote: >> >>> Does anyone know of how I would specify this in my input file for >>> cp2k? Is this possible to do? > > </blockquote></div>