Wow, fantastic vid! :D Really cool to see people putting out such great in depth tutorials. I wanted to clarify one small thing; when you use the 'track orbital' function in IboView, it;s not the energy of the orbital that is being plotted. It's the 'orbital change' i.e. how the centre of charge of the orbital is displaced through space.
Amazing! I am running an aldolic condensation folloing this tutorial and looks great, Can you explain how to increase the number of interpolations to achieve a graph like image 10 from the notes document? thank you again!!!!
Hi there! If your .interp file output from the NEB doesn't happen to have enough steps to provide a smooth graph like the bottom half of image 10, I would recommend dividing the path calculation into smaller fragments, then combining the interp results. So run the NEB between your starting configuration and an intermediary configuration, then again from the intermediate to the finish. Divide into as many chunks as is needed for the desired effect for the energy vs reaction pathway graph. Hope this helps!
Hi, Kate! You mentioned that you optimized both reactants separately and then you brought them together in a single file and optimized them again. Could you tell me how that is done? Thank you and I love the video!
Hello, If you take a look at the walkthrough in the description (also here: docs.google.com/document/d/1YK3ojoLP4Ks7XkJ1ykbOYY7Bsdc66EHvk81AEhAC4Ck/edit?usp=sharing) on page 10 there's a description on how to do geometry optimizations in Avogadro. Also, IaNiusha has a nice video walkthrough on the subject: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-Y1l1PK45Rsg.html Hope this helps!
@@kateboyd1989 I do know how to optimize structures but I was wondering how you can combine single xyz files into one file that allows you to view multiple molecules in one Avogadro window, if that is even possible. I hope that makes sense lol Thank you for your response! It is highly appreciated 😊
@@Liza-gb9mv Oh, gotcha! In Avogadro you can open your two files in separate windows, then use the selection tool (the one that looks like a mouse) to highlight the structure of one of your molecules. Once highlighted, you can copy with crtl+C, head over to the other window, and crtl+V, aka copy/paste. Then you can spend time moving molecules around if you like, or a geometry optimization at that point will move them around for you. Best of luck!
Hi, you have opened image because it was in xyz format but when i tried i got these images in gbw format it's not opening can you please tell how can i see?
That’s a great question. One could theoretically test the proposed product of a reaction by guessing at the reaction mechanism and product structure, running transition state calculations for each guess, and identifying the pathway with the lowest TS energy, which would be the most likely reaction pathway and thus the most likely product.
Hi, your video is quite interesting and clear, but I have a question about the path you describe. During the search process, NEB finds possible "intermediate minima" in different images, and even other "climbing images", what is observed as a second maximum in the image of your path. My question is, can such points be considered additional intermediates and transition states since your reaction is "complex" or is it best to consider a simple scheme containing a single reavtive, product and TS?
Good evening madam, I have the same problem as you because it did not take long for the neb to converge. When I use %geom maxIter 500 end , it's the same as the first output and then I use maxiter 2000 same again... please help me and please show me, how do you change the file.inp? thank you Ms
Thanks so much for the explanation. I am new to these topics but I am very interested in what I am doing research work. Do you carry out consulting? I really appreciate your response. Miguel from Perú
Does anyone have a method of converting Gaussian 16 IRC or opt=modredundant potential energy surface scan to visualize the structures with IboView? Think we really just need a script to convert the structures in the .log file to the combined .xyz trajectory file. In the meantime.... i'll make one
Hi Dr. Kate Boyd. Thank you so much for your training video, very helpful with me. If possible, could you give me your email? I would like to contact you about some of my problems in the TS search mode of ORCA. Now I'm studying a Master's course in Korea about Nanomaterials and I'm a beginner with Computational Chemistry. I hope your reply soon! Thank you so much!