/tech/ - Computational Chemistry

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Computational Chemistry Deckard 2017/09/26 (Tue) 21:32:11 No.1357

Anyone else here study computational (or any other brand of physical) chemistry? What are you reading? Right now I'm a few chapters into Mukamel's Nonlinear Spectroscopy text.

For those who aren't in the field but are interested, I think Szabo and Ostlund's text is a good introduction.

The Plague 2017/10/06 (Fri) 19:02:37 No.1390

Been trying to use GAMESS lately and dear god is the documentation obtuse. Not to mention how touchy the input files are since theyre made to be backwards compatible with literal paper punch-card files.

Is there any other open-source computation software that isn't such a headache to use?

Ishikawa 2017/10/15 (Sun) 18:48:54 No.1407

>>1390
At work we have Schrodinger's suite, which is expensive and proprietary. But, it works well (as it should). In general, computational biology/chemistry/physics is a giant mess when it comes to filetypes. PDB files are literally space dependent, and it's a giant pain to renumber atoms PDB files so that PyMOL can perform accurate RMSD between outputs from various programs.

Laughing Man 2017/10/17 (Tue) 22:53:30 No.1409

File: 1508280810593.jpg (349.69 KB, 700x700, 1429842687822.jpg)

>>1390
Yeah, there aren't many (good) FOS quantum chemistry packages, but I'd recommend taking a look at pyscf ( https://github.com/sunqm/pyscf ). I haven't used it myself, but one of the speakers at a conference I attended a few months ago made it sound ridiculously easy to implement new methodologies in it, and if that's true I can't imagine having too much trouble getting more basic calculations to work in it. I doubt the input files will need to be compatible with punch cards :P

Also >>1407 's mention of file format shenanigans made me remember another useful tool that I actually have used for a long time: http://openbabel.org/wiki/Main_Page OpenBabel is a program that can convert chemistry related data files to and from just about any well known format. I don't think it will set up your entire input file for you, but it definitely helps with manipulating/converting geometries. Enjoy!

Alice Mizuki 2017/11/11 (Sat) 11:14:55 No.1468

>>1390
ORCA is pretty solid. Like GAMESS, but modern. The documentation is much better as well.

The Plague 2018/03/06 (Tue) 16:18:22 No.1703

>tfw cryptominers keeping the graphics card prices high
amd pls think of the science

Saito 2018/07/30 (Mon) 09:29:14 No.1989

Nice to see a chemistry-related thread here! I've just started my MSc in chemistry and somehow got sucked into surface chemistry/physical chemistry and nanosci. Looking for some books from which I can start getting into surface plasmon spectroscopy since I'll be working on building an SPR apparatus for a while. Still haven't found a good book yet.
Computational chemistry seems interesting. It was introduced in my BSc time, but really poorly. What are some "hot topics" that people in computational chemistry are currently working on? And what molecule is that in the OP? I'm guessing pink resembles silicon and yellow resembles phosphorus?