!QM/XTB PBE0 def2-SVP def2/J RIJCOSX DefGrid2 SmallPrint Opt Freq %pal nprocs 16 end #QM/QM calculation using XTB as low-level method. #Nucleophilic attack of iPr-NH2 on acetic-anhidride, in DMF #Optimization restarted from end of previous geometry optimization in the first scan step %maxcore 4096 %scf MaxIter 1000 LShift 1.5 end #N is atom 13, carbonyl C is 2, and initial distance is 5.5 A #I continue last scan from last geometry, because it passed maxiter %geom scan B 2 13 = 4.8, 1.1, 38 end end #Only the amine and the anhidride are treated at high level, the rest at XTB2 %qmmm QMAtoms {0:25} end end %output Print[P_Basis]2 Print[P_MOs]1 end
* xyz 0 1 O -2.369301 -6.342629 -2.195621 O -0.918340 -4.844821 -1.324325 C -2.043387 -5.240163 -1.496055 C -3.277726 -4.573854 -0.973147 H -3.988333 -5.337645 -0.632860 H -3.046690 -3.860170 -0.169104 H -3.730681 -4.022286 -1.812006 O -1.762740 -7.508343 -3.969132 C -1.453946 -7.143325 -2.873838 C -0.141154 -7.410245 -2.209174 H 0.539063 -6.576740 -2.432621 H -0.258546 -7.512044 -1.120779 H 0.256034 -8.337191 -2.636767 N -3.835512 -0.759132 -1.334536 H -3.688864 -1.267809 -0.458183 H -4.730722 -1.108795 -1.696520 C -3.935252 0.670730 -1.059031 H -4.122509 1.173085 -2.027601 C -2.602050 1.181986 -0.528320 C -5.084079 1.043762 -0.126908 H -6.042261 0.698886 -0.544340 H -4.948642 0.560495 0.855117 H -5.154233 2.132852 0.031582 H -2.386284 0.717824 0.448932 H -2.617953 2.273791 -0.385648 H -1.788426 0.924836 -1.222093 H -6.912800 -4.928618 4.291866 O -4.815167 -8.598669 4.657727 C -5.428105 -7.730280 4.062290 H -5.986282 -7.947167 3.135468 N -5.499500 -6.451089 4.420689 C -4.859826 -5.988461 5.631507 H -4.230793 -6.789526 6.015080 H -5.611421 -5.731966 6.380098 H -4.259934 -5.104288 5.418796 C -6.209737 -5.463122 3.652713 H -6.756113 -5.939644 2.841749 H -5.509871 -4.734430 3.237859 H 2.425146 -4.360937 -3.462367 O 4.336005 -2.712052 -0.626748 C 3.735933 -3.208143 -1.561233 H 4.265290 -3.680335 -2.409909 N 2.411350 -3.264294 -1.689794 C 1.553789 -2.700175 -0.674357 H 2.133608 -2.566609 0.237141 H 0.720728 -3.376230 -0.493791 H 1.162539 -1.734365 -1.002076 C 1.763431 -3.704585 -2.899996 H 1.500662 -2.846956 -3.525438 H 0.850020 -4.237292 -2.639586 H -2.656727 -9.030403 3.690747 O -4.087104 -11.264914 0.423297 C -3.271474 -10.557591 0.995792 H -2.606949 -9.872527 0.446102 N -3.083743 -10.514107 2.311610 C -3.868163 -11.335697 3.204351 H -4.584864 -11.897560 2.608607 H -4.390241 -10.698796 3.920441 H -3.220582 -12.029346 3.745384 C -2.139135 -9.624108 2.934438 H -1.694832 -8.967445 2.187475 H -1.348972 -10.198595 3.426185 H 0.409208 -0.658711 1.174378 O -2.994115 -2.235271 1.303343 C -1.857940 -1.790771 1.295253 H -1.231424 -1.842748 0.389050 N -1.254796 -1.174021 2.305537 C -1.888102 -1.044874 3.596735 H -2.809273 -1.624192 3.608763 H -2.116921 0.003256 3.803407 H -1.222254 -1.421555 4.372915 C 0.107026 -0.714698 2.218353 H 0.771645 -1.411701 2.736588 H 0.188672 0.273179 2.675534 H 2.263046 -6.830809 3.875686 O -0.278290 -7.424727 1.167831 C 0.536585 -7.197714 2.041648 H 0.368900 -7.529388 3.083233 N 1.700898 -6.571545 1.889115 C 2.092344 -6.020254 0.612781 H 1.232608 -6.033188 -0.053267 H 2.899965 -6.611709 0.173777 H 2.435073 -4.995758 0.752723 C 2.568466 -6.267229 2.996362 H 2.517867 -5.198547 3.220949 H 3.596632 -6.528786 2.742422 H -5.886497 -10.413018 -0.369579 O -7.916291 -7.063213 1.279620 C -7.826754 -8.111393 0.657554 H -8.690766 -8.792312 0.560091 N -6.742489 -8.558501 0.039923 C -5.505082 -7.813365 0.074282 H -5.677971 -6.875649 0.599179 H -5.159406 -7.617591 -0.941726 H -4.734617 -8.387194 0.591725 C -6.715844 -9.790220 -0.710846 H -6.579573 -9.572532 -1.772157 H -7.651189 -10.328414 -0.572726 H -1.615861 -0.206018 -4.971968 O -2.213060 -4.190305 -3.861735 C -1.799547 -3.289067 -4.568988 H -1.754959 -3.398269 -5.671705 N -1.360201 -2.106455 -4.152096 C -1.330459 -1.785165 -2.740401 H -1.196386 -2.704282 -2.176908 H -2.268138 -1.312731 -2.406242 H -0.492358 -1.114498 -2.563588 C -0.938198 -1.060329 -5.047513 H -0.933358 -1.422733 -6.074287 H 0.066249 -0.723977 -4.780737 H -7.593502 -5.145501 -0.068814 O -8.350613 -2.955680 2.882767 C -8.155279 -3.625148 1.881029 H -8.702899 -4.565203 1.699455 N -7.286998 -3.343960 0.917063 C -6.496533 -2.134309 0.937666 H -6.898857 -1.471230 1.701009 H -6.555841 -1.656202 -0.039480 H -5.451254 -2.359239 1.162022 C -7.128394 -4.178018 -0.244999 H -6.066661 -4.310171 -0.450777 H -7.583895 -3.701211 -1.115914 H -5.138627 -10.816017 -3.400509 O -2.280665 -9.008386 -1.767450 C -3.200753 -9.595783 -2.308276 H -4.090976 -9.063143 -2.670484 N -3.240305 -10.902903 -2.558486 C -2.167634 -11.764576 -2.125979 H -1.349068 -11.136978 -1.779205 H -1.829976 -12.387228 -2.956658 H -2.507331 -12.402992 -1.307711 C -4.411925 -11.556964 -3.075211 H -4.862477 -12.179870 -2.297898 H -4.140387 -12.190722 -3.922826 H -2.887443 -6.161808 3.171757 O 0.632730 -3.720844 2.762464 C -0.354232 -4.302077 2.339580 H -0.494854 -4.503406 1.266018 N -1.352785 -4.769208 3.084848 C -1.381549 -4.542989 4.511574 H -0.457239 -4.041844 4.792591 H -1.452418 -5.496161 5.040022 H -2.235670 -3.917502 4.777375 C -2.515099 -5.388188 2.500723 H -2.248952 -5.847938 1.550540 H -3.299098 -4.643227 2.339877 H -10.349903 -7.612282 4.259151 O -8.184161 -5.293783 7.068909 C -8.373718 -6.201324 6.281356 H -7.841307 -7.166488 6.366999 N -9.213264 -6.169501 5.246621 C -10.009636 -4.989629 4.986812 H -10.083619 -4.416440 5.909178 H -11.006888 -5.287665 4.664535 H -9.552294 -4.362262 4.217991 C -9.320458 -7.246665 4.297734 H -8.666599 -8.065478 4.593125 H -9.030270 -6.909504 3.299555 H -8.151127 -3.026184 6.488185 O -4.205022 -2.765220 5.012550 C -5.396279 -2.492355 5.003729 H -5.916174 -2.207759 4.075213 N -6.198913 -2.504148 6.061747 C -5.706200 -2.854126 7.372700 H -4.646814 -3.089947 7.293395 H -6.256989 -3.716349 7.753136 H -5.842051 -2.017265 8.061239 C -7.610633 -2.228584 5.976365 H -7.925918 -2.193066 4.935562 H -7.844099 -1.277362 6.462278 H -6.355251 -2.091271 -6.743799 O -6.316564 -1.730360 -2.551717 C -6.480898 -2.302411 -3.616016 H -7.247392 -3.082233 -3.742672 N -5.792993 -2.077788 -4.734813 C -4.735449 -1.096304 -4.793760 H -4.533535 -0.728658 -3.791245 H -5.024341 -0.262730 -5.439109 H -3.832855 -1.559778 -5.194069 C -6.055222 -2.789894 -5.958290 H -6.849794 -3.517241 -5.804977 H -5.149149 -3.308248 -6.284614 H 4.080115 -0.431905 -0.479105 O 1.798262 -0.062870 -3.460933 C 2.611743 -0.095271 -2.557205 H 3.504319 -0.740834 -2.595580 N 2.533195 0.604795 -1.422196 C 1.472081 1.566275 -1.230386 H 0.874077 1.597256 -2.139774 H 1.889972 2.556432 -1.038563 H 0.837182 1.281943 -0.387446 C 3.508381 0.487766 -0.366212 H 2.996189 0.456934 0.596203 H 4.190788 1.341571 -0.369987 H -4.170860 -7.564925 -6.729657 O -6.274485 -8.667126 -3.814517 C -5.584634 -8.291503 -4.753991 H -5.381152 -8.963416 -5.608005 N -5.020130 -7.103561 -4.884631 C -5.142387 -6.089012 -3.862875 H -5.521290 -6.551244 -2.954154 H -5.840555 -5.313456 -4.184585 H -4.162762 -5.652068 -3.672988 C -4.160225 -6.767971 -5.988550 H -3.140740 -6.634449 -5.619534 H -4.504032 -5.840819 -6.451736 H -9.626858 -8.461905 -5.428183 O -8.154907 -5.027356 -4.980753 C -8.630450 -6.139637 -5.119295 H -8.880507 -6.538473 -6.119240 N -8.925216 -6.986855 -4.137510 C -8.617837 -6.660770 -2.764689 H -8.265464 -5.632820 -2.727250 H -7.840624 -7.331487 -2.396698 H -9.509639 -6.765912 -2.144073 C -9.388007 -8.328699 -4.374189 H -10.282696 -8.523937 -3.777541 H -8.607699 -9.039643 -4.088847 *
I want to investigate the geometrical change of azobenzene from trans isomer to cis isomer through the relaxed scan PES by scanning the C-N=N-C. I tried based on the orca 6.0 manual but the atoms become spread out. Could you help to find out how to it? Thank you in advance
can you post your input file? remember that you have to choose your starting parameter of the scan very close to the actual value in the starting structure. And dihedral angles have to be defined in a certain order, so the numbering of the atoms has to be kept the same in the %geom scan D X1 X2 X3 X4 = startAngle, endAngle, nsteps end end block as it was measured manually by you in the geometry. You have to also check that your starting geometry is realistic and doesn't contain atoms bonded in a weird manner.
because I am trying to do the same thing, I wanted to repeat your QM / xtb calculation also, I wanted to know if you used 17 molecules of dimethylformamide
Awesome video! I am working on a small system where the concern is on charged species. Whenever I try to run for charged species that is in input line I type "xyz 1 2" it always give me an error but when I use the same model for neutral state, it runs smoothly. Any tips would be appreciated.
@@jimitpatel5651 whenever you change the charge you have to change the multiplicity accordingly. You may have a singlet charged species and a doublet neutral one.
@@niconeuman Thanks for the reply! I am using single charged species as my model has 1 unpaired electron and according to the formula of multiplicity which is 2S+1, the multiplicity should be 2 and thats what I am using.
@@jimitpatel5651 if you get an error regarding multiplicity, check that you are not missing or have extra H. Sometimes drawing software autocompletes H atoms and it gets it wrong.
@@juancamilorodriguezbetanco4079 yes I know how to do that. But my experience isn't very good, because you need to use very small integration steps to avoid H atoma flying off. I have started doing MD with XTB, and it works really well. And it is very simple to do.
@@niconeuman Muchas gracias Nicolas, tu sabes si de alguna forma con QM/QM o QM/MM puedo calcular a cada timestep un tddft?, para modelar un hamiltoniano dependiente del tiempo
Thank you! For editing structures and looking at optimized geometries, orbitals, etc, y use chemcraft. For analysis I use Octave or Origin, depending on the complexity of the analysis.
Hi. Thanks for your useful video. I got an error that there is no otool_xtb in orca binary path. How can I solve it? Any comments would be appreciated.
You have to add the path to where the xtb binary is installed. If you use a shell file for submitting your calculation it is something like: echo $PATH path/to/xtb. But I don't remember exactly. In the xtb web page there are some instructions. It is basically telling orca where xtb is installed.
@@niconeuman I just solved the problem by using below command: ln -s $(which xtb) otool_xtb thanks for your time. please share more video on QM/MM with orca. Cheers
!QM/XTB PBE0 def2-SVP def2/J RIJCOSX DefGrid2 SmallPrint Opt Freq
%pal nprocs 16 end
#QM/QM calculation using XTB as low-level method.
#Nucleophilic attack of iPr-NH2 on acetic-anhidride, in DMF
#Optimization restarted from end of previous geometry optimization in the first scan step
%maxcore 4096
%scf MaxIter 1000
LShift 1.5
end
#N is atom 13, carbonyl C is 2, and initial distance is 5.5 A
#I continue last scan from last geometry, because it passed maxiter
%geom scan B 2 13 = 4.8, 1.1, 38 end end
#Only the amine and the anhidride are treated at high level, the rest at XTB2
%qmmm
QMAtoms {0:25} end
end
%output
Print[P_Basis]2
Print[P_MOs]1
end
* xyz 0 1
O -2.369301 -6.342629 -2.195621
O -0.918340 -4.844821 -1.324325
C -2.043387 -5.240163 -1.496055
C -3.277726 -4.573854 -0.973147
H -3.988333 -5.337645 -0.632860
H -3.046690 -3.860170 -0.169104
H -3.730681 -4.022286 -1.812006
O -1.762740 -7.508343 -3.969132
C -1.453946 -7.143325 -2.873838
C -0.141154 -7.410245 -2.209174
H 0.539063 -6.576740 -2.432621
H -0.258546 -7.512044 -1.120779
H 0.256034 -8.337191 -2.636767
N -3.835512 -0.759132 -1.334536
H -3.688864 -1.267809 -0.458183
H -4.730722 -1.108795 -1.696520
C -3.935252 0.670730 -1.059031
H -4.122509 1.173085 -2.027601
C -2.602050 1.181986 -0.528320
C -5.084079 1.043762 -0.126908
H -6.042261 0.698886 -0.544340
H -4.948642 0.560495 0.855117
H -5.154233 2.132852 0.031582
H -2.386284 0.717824 0.448932
H -2.617953 2.273791 -0.385648
H -1.788426 0.924836 -1.222093
H -6.912800 -4.928618 4.291866
O -4.815167 -8.598669 4.657727
C -5.428105 -7.730280 4.062290
H -5.986282 -7.947167 3.135468
N -5.499500 -6.451089 4.420689
C -4.859826 -5.988461 5.631507
H -4.230793 -6.789526 6.015080
H -5.611421 -5.731966 6.380098
H -4.259934 -5.104288 5.418796
C -6.209737 -5.463122 3.652713
H -6.756113 -5.939644 2.841749
H -5.509871 -4.734430 3.237859
H 2.425146 -4.360937 -3.462367
O 4.336005 -2.712052 -0.626748
C 3.735933 -3.208143 -1.561233
H 4.265290 -3.680335 -2.409909
N 2.411350 -3.264294 -1.689794
C 1.553789 -2.700175 -0.674357
H 2.133608 -2.566609 0.237141
H 0.720728 -3.376230 -0.493791
H 1.162539 -1.734365 -1.002076
C 1.763431 -3.704585 -2.899996
H 1.500662 -2.846956 -3.525438
H 0.850020 -4.237292 -2.639586
H -2.656727 -9.030403 3.690747
O -4.087104 -11.264914 0.423297
C -3.271474 -10.557591 0.995792
H -2.606949 -9.872527 0.446102
N -3.083743 -10.514107 2.311610
C -3.868163 -11.335697 3.204351
H -4.584864 -11.897560 2.608607
H -4.390241 -10.698796 3.920441
H -3.220582 -12.029346 3.745384
C -2.139135 -9.624108 2.934438
H -1.694832 -8.967445 2.187475
H -1.348972 -10.198595 3.426185
H 0.409208 -0.658711 1.174378
O -2.994115 -2.235271 1.303343
C -1.857940 -1.790771 1.295253
H -1.231424 -1.842748 0.389050
N -1.254796 -1.174021 2.305537
C -1.888102 -1.044874 3.596735
H -2.809273 -1.624192 3.608763
H -2.116921 0.003256 3.803407
H -1.222254 -1.421555 4.372915
C 0.107026 -0.714698 2.218353
H 0.771645 -1.411701 2.736588
H 0.188672 0.273179 2.675534
H 2.263046 -6.830809 3.875686
O -0.278290 -7.424727 1.167831
C 0.536585 -7.197714 2.041648
H 0.368900 -7.529388 3.083233
N 1.700898 -6.571545 1.889115
C 2.092344 -6.020254 0.612781
H 1.232608 -6.033188 -0.053267
H 2.899965 -6.611709 0.173777
H 2.435073 -4.995758 0.752723
C 2.568466 -6.267229 2.996362
H 2.517867 -5.198547 3.220949
H 3.596632 -6.528786 2.742422
H -5.886497 -10.413018 -0.369579
O -7.916291 -7.063213 1.279620
C -7.826754 -8.111393 0.657554
H -8.690766 -8.792312 0.560091
N -6.742489 -8.558501 0.039923
C -5.505082 -7.813365 0.074282
H -5.677971 -6.875649 0.599179
H -5.159406 -7.617591 -0.941726
H -4.734617 -8.387194 0.591725
C -6.715844 -9.790220 -0.710846
H -6.579573 -9.572532 -1.772157
H -7.651189 -10.328414 -0.572726
H -1.615861 -0.206018 -4.971968
O -2.213060 -4.190305 -3.861735
C -1.799547 -3.289067 -4.568988
H -1.754959 -3.398269 -5.671705
N -1.360201 -2.106455 -4.152096
C -1.330459 -1.785165 -2.740401
H -1.196386 -2.704282 -2.176908
H -2.268138 -1.312731 -2.406242
H -0.492358 -1.114498 -2.563588
C -0.938198 -1.060329 -5.047513
H -0.933358 -1.422733 -6.074287
H 0.066249 -0.723977 -4.780737
H -7.593502 -5.145501 -0.068814
O -8.350613 -2.955680 2.882767
C -8.155279 -3.625148 1.881029
H -8.702899 -4.565203 1.699455
N -7.286998 -3.343960 0.917063
C -6.496533 -2.134309 0.937666
H -6.898857 -1.471230 1.701009
H -6.555841 -1.656202 -0.039480
H -5.451254 -2.359239 1.162022
C -7.128394 -4.178018 -0.244999
H -6.066661 -4.310171 -0.450777
H -7.583895 -3.701211 -1.115914
H -5.138627 -10.816017 -3.400509
O -2.280665 -9.008386 -1.767450
C -3.200753 -9.595783 -2.308276
H -4.090976 -9.063143 -2.670484
N -3.240305 -10.902903 -2.558486
C -2.167634 -11.764576 -2.125979
H -1.349068 -11.136978 -1.779205
H -1.829976 -12.387228 -2.956658
H -2.507331 -12.402992 -1.307711
C -4.411925 -11.556964 -3.075211
H -4.862477 -12.179870 -2.297898
H -4.140387 -12.190722 -3.922826
H -2.887443 -6.161808 3.171757
O 0.632730 -3.720844 2.762464
C -0.354232 -4.302077 2.339580
H -0.494854 -4.503406 1.266018
N -1.352785 -4.769208 3.084848
C -1.381549 -4.542989 4.511574
H -0.457239 -4.041844 4.792591
H -1.452418 -5.496161 5.040022
H -2.235670 -3.917502 4.777375
C -2.515099 -5.388188 2.500723
H -2.248952 -5.847938 1.550540
H -3.299098 -4.643227 2.339877
H -10.349903 -7.612282 4.259151
O -8.184161 -5.293783 7.068909
C -8.373718 -6.201324 6.281356
H -7.841307 -7.166488 6.366999
N -9.213264 -6.169501 5.246621
C -10.009636 -4.989629 4.986812
H -10.083619 -4.416440 5.909178
H -11.006888 -5.287665 4.664535
H -9.552294 -4.362262 4.217991
C -9.320458 -7.246665 4.297734
H -8.666599 -8.065478 4.593125
H -9.030270 -6.909504 3.299555
H -8.151127 -3.026184 6.488185
O -4.205022 -2.765220 5.012550
C -5.396279 -2.492355 5.003729
H -5.916174 -2.207759 4.075213
N -6.198913 -2.504148 6.061747
C -5.706200 -2.854126 7.372700
H -4.646814 -3.089947 7.293395
H -6.256989 -3.716349 7.753136
H -5.842051 -2.017265 8.061239
C -7.610633 -2.228584 5.976365
H -7.925918 -2.193066 4.935562
H -7.844099 -1.277362 6.462278
H -6.355251 -2.091271 -6.743799
O -6.316564 -1.730360 -2.551717
C -6.480898 -2.302411 -3.616016
H -7.247392 -3.082233 -3.742672
N -5.792993 -2.077788 -4.734813
C -4.735449 -1.096304 -4.793760
H -4.533535 -0.728658 -3.791245
H -5.024341 -0.262730 -5.439109
H -3.832855 -1.559778 -5.194069
C -6.055222 -2.789894 -5.958290
H -6.849794 -3.517241 -5.804977
H -5.149149 -3.308248 -6.284614
H 4.080115 -0.431905 -0.479105
O 1.798262 -0.062870 -3.460933
C 2.611743 -0.095271 -2.557205
H 3.504319 -0.740834 -2.595580
N 2.533195 0.604795 -1.422196
C 1.472081 1.566275 -1.230386
H 0.874077 1.597256 -2.139774
H 1.889972 2.556432 -1.038563
H 0.837182 1.281943 -0.387446
C 3.508381 0.487766 -0.366212
H 2.996189 0.456934 0.596203
H 4.190788 1.341571 -0.369987
H -4.170860 -7.564925 -6.729657
O -6.274485 -8.667126 -3.814517
C -5.584634 -8.291503 -4.753991
H -5.381152 -8.963416 -5.608005
N -5.020130 -7.103561 -4.884631
C -5.142387 -6.089012 -3.862875
H -5.521290 -6.551244 -2.954154
H -5.840555 -5.313456 -4.184585
H -4.162762 -5.652068 -3.672988
C -4.160225 -6.767971 -5.988550
H -3.140740 -6.634449 -5.619534
H -4.504032 -5.840819 -6.451736
H -9.626858 -8.461905 -5.428183
O -8.154907 -5.027356 -4.980753
C -8.630450 -6.139637 -5.119295
H -8.880507 -6.538473 -6.119240
N -8.925216 -6.986855 -4.137510
C -8.617837 -6.660770 -2.764689
H -8.265464 -5.632820 -2.727250
H -7.840624 -7.331487 -2.396698
H -9.509639 -6.765912 -2.144073
C -9.388007 -8.328699 -4.374189
H -10.282696 -8.523937 -3.777541
H -8.607699 -9.039643 -4.088847
*
Thank you, thank you, thank you so much, thank you one thousand, and thank you.
Thank you!
I want to investigate the geometrical change of azobenzene from trans isomer to cis isomer through the relaxed scan PES by scanning the C-N=N-C. I tried based on the orca 6.0 manual but the atoms become spread out. Could you help to find out how to it? Thank you in advance
can you post your input file? remember that you have to choose your starting parameter of the scan very close to the actual value in the starting structure. And dihedral angles have to be defined in a certain order, so the numbering of the atoms has to be kept the same in the %geom scan D X1 X2 X3 X4 = startAngle, endAngle, nsteps end end block as it was measured manually by you in the geometry. You have to also check that your starting geometry is realistic and doesn't contain atoms bonded in a weird manner.
@@niconeuman here is my input file
! B3LYP/G SV(P) Opt
%geom Scan
D 12 1 0 2 = 0, 180, 20
end
end
%pal
nprocs=8
end
%geom
MaxIter 300
end
%maxcore 1000
* int 0 1
N 0 0 0 0.000000000000 0.00000000 0.00000000
N 1 0 0 1.266212383438 0.00000000 0.00000000
C 1 2 0 1.378981204254 117.20832184 0.00000000
C 3 1 2 1.400689891494 123.41602545 335.06193366
C 3 1 2 1.398810895176 116.92243025 159.35870397
C 4 3 1 1.378703516425 119.93606890 184.06469816
H 4 3 1 1.079927549392 118.51784199 3.08408358
C 5 3 1 1.379423938565 119.96412006 177.03697458
H 5 3 1 1.079227002580 118.71786405 355.80968604
C 8 5 3 1.387568304715 120.20655369 358.83101785
H 6 4 3 1.080527919087 119.89899534 179.56516009
H 8 5 3 1.080183199728 119.89190223 179.29313228
C 2 1 3 1.378864021494 117.22366116 173.20881150
C 13 2 1 1.400702595310 123.38901527 334.83464699
C 13 2 1 1.398825154455 116.94926313 159.18151291
C 14 13 2 1.378713401158 119.94220931 184.14170289
H 14 13 2 1.079932074898 118.50950251 3.13871165
C 15 13 2 1.379391265486 119.96188778 176.96998043
H 15 13 2 1.079240021639 118.72544357 355.72308974
C 18 15 13 1.387580919213 120.21187199 358.83056176
H 16 14 13 1.080511162223 119.90139949 179.58031757
H 18 15 13 1.080203428586 119.89821312 179.29368094
H 20 18 15 1.080027199443 119.92964397 180.73298357
H 10 8 5 1.080027738999 119.93408666 180.70163219
*
Honestly, your video is very important; thank you for your time and effort.
Could you please provide me with your input file?
@@hamzaallal1867 I have to look for it.
I pinned the comment with the code, and the response contains the coordinates. It was a long file.
Cool vid :) xTB has really changed what's feasible for quick calculations on large systems
Yes it really surprised me when I first tested it!
because I am trying to do the same thing, I wanted to repeat your QM / xtb calculation
also, I wanted to know if you used 17 molecules of dimethylformamide
Awesome video! I am working on a small system where the concern is on charged species. Whenever I try to run for charged species that is in input line I type "xyz 1 2" it always give me an error but when I use the same model for neutral state, it runs smoothly. Any tips would be appreciated.
@@jimitpatel5651 whenever you change the charge you have to change the multiplicity accordingly. You may have a singlet charged species and a doublet neutral one.
@@niconeuman Thanks for the reply! I am using single charged species as my model has 1 unpaired electron and according to the formula of multiplicity which is 2S+1, the multiplicity should be 2 and thats what I am using.
@@jimitpatel5651 if you get an error regarding multiplicity, check that you are not missing or have extra H. Sometimes drawing software autocompletes H atoms and it gets it wrong.
Hi Nicolas, do you know how to perform Ab Initio Moledular Dynamics (AIMD) calculations with ORCA 6.0.1?
@@juancamilorodriguezbetanco4079 yes I know how to do that. But my experience isn't very good, because you need to use very small integration steps to avoid H atoma flying off. I have started doing MD with XTB, and it works really well. And it is very simple to do.
@@niconeuman Muchas gracias Nicolas, tu sabes si de alguna forma con QM/QM o QM/MM puedo calcular a cada timestep un tddft?, para modelar un hamiltoniano dependiente del tiempo
very useful video, thank you for the explanation! what software do you use geometry setup and to check the results?
Thank you! For editing structures and looking at optimized geometries, orbitals, etc, y use chemcraft. For analysis I use Octave or Origin, depending on the complexity of the analysis.
@@niconeumanThanks! I used to use Chemcraft, but it wasn't a really good editor Maybe I should check it out again
Hi. Thanks for your useful video. I got an error that there is no otool_xtb in orca binary path. How can I solve it? Any comments would be appreciated.
You have to add the path to where the xtb binary is installed. If you use a shell file for submitting your calculation it is something like: echo $PATH path/to/xtb. But I don't remember exactly. In the xtb web page there are some instructions. It is basically telling orca where xtb is installed.
@@niconeuman I already did it, but still have the problem. Do you have otool_xtb in Orca directory?
@@niconeuman I just solved the problem by using below command:
ln -s $(which xtb) otool_xtb
thanks for your time.
please share more video on QM/MM with orca. Cheers
Very Good explanation. Is it possible to run MD also using QM/XTB?
Yes it is possible. I haven't done a video on MD but the syntax is easy, the manual explains it well.
@@niconeuman Thank you. Could you please send me a syntax example for running MD using QM/MM?