Avogadro with Gaussian IRC calculation

[@alexandrevoute9921]

Thank you very much for the tutorial! I have just a couple of questions about displaying the result of an IRC calculation: 1/ Does one just need to open the IRC file and go to 'Animations', in order to display all the different steps as frames of an animation? Or should one do extra manipulation of the output? (I ask this because I get only one frame instead of all the 100 I calculated...) 2/ If one wants to see the whole reaction: since by default Gaussian explores both directions (and puts them in the right order in the output file), would it not be easier to not specify it (i.e. not provide the forward/backward options)?

[@eyeshidden]

Hi! IaNiusha I have a problem reading IRC Path in avogadro, I calculated my IRC in Gaussian, but when I open .out file in Avogadro, the software open only one frame. Help me please :)

[@ArabyGUC]

You can write a simple bash script to concatenate the IRC portions. You basically identify the section you want to copy with sed for instance and paste it one by one in reverse order.

[@englishmasteryhub7]

thanks for this vedio and I am a little bit new in computional chemistry

[@zelimirvulic]

great video. Could you prepare the same sort of video using US-GAMESS program. There is no need for students to buy Gaussian licence just to study at their classes

[@jiayuerong386]

Did you find out how to visilize pathway using GAMESS? Thanks

[@emonreturns7811]

I really appreciate your explanation. You make it so easy to understand. Thank you so much for that. But why you don't you demonstrate Gaussian software? Its makes it harder on those parts to understand. I am a Bioinformatician. I have a very little knowledge about the scripting in Gaussian.

[@tmartin9482]

Thanks for the tutorial! Why are you actually using increased convergence criteria and a fine grid for the IRC calculation? I would fall back to the same level of accuracy as with the transition state optimization. And I think direct SCF is default in G09, which makes this option for the SCF keyword obsolete.

[@IaNiusha]

Cause sometimes the PES is kind of flat, so the calculation can lose track. If the same level of accuracyworks, good for you!

[@LVCIVSANTONIVS]

Thanks for the video.. by the way are u using the gaussian 09?

[@IaNiusha]

yes!

[@quantumjuanchy]

Thanks for the video !!! One question if you will do the calculation for this reaction HSO4- + CH3OH >> H2O + CH2O + HSO3- how you will draw the products ? will you do a intermediate with the water or you will have 3 independent molecules ?. Thank you before hand !!

[@IaNiusha]

+quantumjuanchy you'd have to to the intermediate. it's one step at a time really.

[@mdsultanmahmud9947]

How do I create reactant complex and product complex for this reaction using Avogadro?

[@salcordirsdoso3286]

Hi IaNiusha, I really appreciate your effort you are putting in this. It really helped me a lot so far. You suggested to use Janpa to generate NAO. I am using Win10 and i have issues to start Janpa. I would be deeply grateful if you could make a video for Janpa using orca as a ESS. I dont know how to get the .47 file.

[@IaNiusha]

+salcordirs doso yeah, it's coming eventually. When I have some time =)

[@salcordirsdoso3286]

+IaNiusha Thank you very much:D

[@javeed7887]

Thanks for uploading, appreciative..

[@dr.shivarajmaidur7198]

Hi IaNiusha, Can you upload a video regarding florescence spectra computation using Gaussian 09. That would be great if you could do it, and I heartily appreciate your effort in making these amazing videos. Looking forward for emission spectra.

[@IaNiusha]

You can watch this video: kzbin.info/www/bejne/Z2SYoKaklq1ke6c

[@dr.shivarajmaidur7198]

Dear madam, Thank you very much. Could you please send your email ID, I wanna be in touch with you for some helps. Its my email ID just say hi to: [e-mail]

[@johanmendoza96]

Hello IaNiusha I have a problem running a IRC calculation on Gaussian 09, I already found the TS but when I run it get two minimums (reactants and products) but they aren't minimums, because after IRC calculation I performed a optimization and the structure change to another with less energy. I use this keywords: #irc=(maxpoints=500,recalc=2,calcfc,maxcycle=40,cartesian,lqa,stepsize=8,tight) b3lyp/gen int=(acc2e=12,grid=ultrafine) pseudo=read scf=xqc

[@IaNiusha]

+Johan Mendoza that's ok, the IRC by default computes single points following the vector defined by the imaginary frequency of the TS. When the calculation stops it's wither because you have reached the max number of steps, or because the change in SP energies is small. But these steps are not optimized structures so when you run an OPT on the finial geometry you might end up with a slightly different structure.

[@johanmendoza96]

+IaNiusha Yes, but I increased the number of steps, the IRC output has only 11 points, and I need to reach the minimum. What can I do?

[@IaNiusha]

+Johan Mendoza you run an optimization on the output of your IRC

[@johanmendoza96]

+IaNiusha Yes, I took both structures (reactants and products) and then I ran an optimization calculation

[@IaNiusha]

+Johan Mendoza so what's the problem?

[@Avabelieve]

7:20 - IRC calculation

[@johanmendoza96]

Thanks for sharing, It was so helpful, Can I ask you for a favor? Can you upload a video explaining how to manage a cluster metal?

[@IaNiusha]

This depends on the software available and the size/type of cluster you want to look at. Can you give me an example?

[@johanmendoza96]

IaNiusha Look, we have a LINUX computer cluster loaded with Gaussian 09, and I want to reproduce an aggregate of 7 Platinum atoms, I tried to handle it with different spin multiplicities, but there are some work with isotopes pt (111 and 110) published. I would like to do something similar to this article: www.sciencedirect.com/science/article/pii/S2210271X14000103

[@johanmendoza96]

IaNiusha beforehand thank you very much for everything, has been of great help, regards from Mexico

[@IaNiusha]

Johan Mendoza well, too bad they don't provide the cartesian coordinates, so you need to use internal coordinates and adjust our bond lengths to the ones on their figures. Isotopes are defined in the general atom-coordinates field as so: C(Iso=13,Spin=3) x y z They give you a DFT and their basis set, very convenient. What is your difficulty more precisely?

[@johanmendoza96]

IaNiusha Thank you very much. I was wrong to think of the Pt as an isotope, the term Pt (111) is related to the glass surface of Pt. Anyway I have to work with the multiplicity of Pt atoms, and I am not sure if the input file must be written as multiplicity located at the origin like: 0 3 Pt(Spin=3) 0.40617104 -0.19806750 1.29082717 Pt(Spin=3) 0.20209404 -0.01918086 -1.94990311 Pt(Spin=3) 3.29880099 -1.66079008 1.02792940 Pt(Spin=3) 2.81673053 1.25989445 -0.41222111 Pt(Spin=3) 0.68416451 -2.93986539 -0.50975260 Pt(Spin=3) 3.09472399 -1.48190344 -2.21280088 or only: 0 3 Pt 0.40617104 -0.19806750 1.29082717 Pt 0.20209404 -0.01918086 -1.94990311 Pt 3.29880099 -1.66079008 1.02792940 Pt 2.81673053 1.25989445 -0.41222111 Pt 0.68416451 -2.93986539 -0.50975260 Pt 3.09472399 -1.48190344 -2.21280088

[@khuloodobaid-4856]

thank you that is good