You have no idea how important this kind of videos that you're doing are for those of us just learning chemistry. I'm hoping that you have a long series planned.
@@DrBenChem I'm just starting out with chemistry, physics and computational stuff, so I'm not even qualified to know what I want to know. But maybe you could make a video where you look over some real life IR spectrum graphs and pretend you don't know what the sample was, then interpret the graphs...
4 ปีที่แล้ว +1
Speed tip that Dr. Ben was probably going to disclose anyway in one of the next videos: After the main Orca calculation is completed (Optimize + Vib. Freq.), you can just open directly output.log in Avogadro and see both the animations and the graph there. In the "Visualization and printing" section from the Orca forum there's a list of all the programs that can interact with Orca output: sites.google.com/site/orcainputlibrary/printing-and-visualization
4 ปีที่แล้ว
A speed tip: In Windows, from File Explorer, click in the address bar to select its contents; then type cmd and press Enter. That opens a non-admin Command Prompt session in the current folder!
4 ปีที่แล้ว +1
I've read more about why and how molecules vibrate on Wikipedia. A question that popped into my mind was "why don't they stop vibrating after a while"? Here's the answer, for whoever might have the same question: there's no friction at that level, and also remember about conservation of energy... so yeah, no reason for them to stop.
4 ปีที่แล้ว
Another good resource for me today to better understand molecular vibrations has been this video, which looks like it was made 60 years ago: th-cam.com/video/3RqEIr8NtMI/w-d-xo.html Especially in the final minutes when it all comes together, it has very good info. An interesting tidbit was that molecules can actually lose amplitude in one of their normal modes of vibration and emit the energy lost as an electromagnetic wave, just as photons do when they "fall down" to a lower energy state. Interesting!
Thanks DrBen for the tutorials....easy to assimilate.....besides jmol what other free softwares can do the job.....i spent so many hours on installing jmol without any success
Another speed tip, for those who don't want to learn how to create input files for Orca, but still need them: You go to WebMO and log in with guest:guest www.webmo.net/demoserver/cgi-bin/webmo/login.cgi Create a new task, which will fail most likely because there's too much calculation to be done for the free tier. Then, you select the job and download its "Job Archive". In it, you'll find "input.inp" which you will feed to your own Orca installation. Super-tip: you can actually do this for any computation engine that they support! No need to learn how to create those damn input files. Super-tip #2: you can also create input files for many computational engines with Avogadro, from the Extensions menu.
Thanks, super useful additions! I've used GitHub to host input files used in this series, so that people can easily download them rather than make them if preferred.
You have no idea how important this kind of videos that you're doing are for those of us just learning chemistry. I'm hoping that you have a long series planned.
I have a few more videos planned, yes! Thanks for the feedback and tips, I really appreciate it!
@@DrBenChem I know you're probably a very busy dude, but if you could give us one video per week it would be amazing. Or one per 10 days... :-S
@ Any requests for subjects to cover?
@@DrBenChem I'm just starting out with chemistry, physics and computational stuff, so I'm not even qualified to know what I want to know.
But maybe you could make a video where you look over some real life IR spectrum graphs and pretend you don't know what the sample was, then interpret the graphs...
Speed tip that Dr. Ben was probably going to disclose anyway in one of the next videos:
After the main Orca calculation is completed (Optimize + Vib. Freq.), you can just open directly output.log in Avogadro and see both the animations and the graph there.
In the "Visualization and printing" section from the Orca forum there's a list of all the programs that can interact with Orca output: sites.google.com/site/orcainputlibrary/printing-and-visualization
A speed tip:
In Windows, from File Explorer, click in the address bar to select its contents; then type cmd and press Enter. That opens a non-admin Command Prompt session in the current folder!
I've read more about why and how molecules vibrate on Wikipedia. A question that popped into my mind was "why don't they stop vibrating after a while"? Here's the answer, for whoever might have the same question: there's no friction at that level, and also remember about conservation of energy... so yeah, no reason for them to stop.
Another good resource for me today to better understand molecular vibrations has been this video, which looks like it was made 60 years ago: th-cam.com/video/3RqEIr8NtMI/w-d-xo.html
Especially in the final minutes when it all comes together, it has very good info.
An interesting tidbit was that molecules can actually lose amplitude in one of their normal modes of vibration and emit the energy lost as an electromagnetic wave, just as photons do when they "fall down" to a lower energy state. Interesting!
Thanks DrBen for the tutorials....easy to assimilate.....besides jmol what other free softwares can do the job.....i spent so many hours on installing jmol without any success
Hi! I'm afraid I don't know offhand any other software but I can have a look. What problems are you having running Jmol?
@@DrBenChem I am unable to install it on my laptop.
Thank You so much ... I was just looking for same
Just glad I could help!
Another speed tip, for those who don't want to learn how to create input files for Orca, but still need them:
You go to WebMO and log in with guest:guest www.webmo.net/demoserver/cgi-bin/webmo/login.cgi
Create a new task, which will fail most likely because there's too much calculation to be done for the free tier. Then, you select the job and download its "Job Archive". In it, you'll find "input.inp" which you will feed to your own Orca installation.
Super-tip: you can actually do this for any computation engine that they support! No need to learn how to create those damn input files.
Super-tip #2: you can also create input files for many computational engines with Avogadro, from the Extensions menu.
Thanks, super useful additions!
I've used GitHub to host input files used in this series, so that people can easily download them rather than make them if preferred.