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Harm Reduction Notes for the COVID-19 Pandemic

Molecular sandbox

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!/sly9iFJgg - Wed, 22 Jun 2016 14:54:50 EST H8Fdbu5S No.77990
File: 1466621690969.png -(291146B / 284.32KB, 1271x969) Thumbnail displayed, click image for full size. Molecular sandbox
I found a great free molecular simulator, at http://avogadro.cc/wiki/Main_Page . It's real easy to use, but the fucking thing crashes without warning or apparent reason. There's seemingly nothing I can do to make it run. The only circumstance it DOESN'T crash in is when I first load it and haven't added any atoms/loaded a save.

So unless y'all have a fix that I haven't tried, I'm looking for a program with a similar sandbox-style modeling.
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PotatoSamurai !/sly9iFJgg - Wed, 22 Jun 2016 14:59:02 EST H8Fdbu5S No.77991 Reply
1466621942644.png -(187821B / 183.42KB, 1265x979) Thumbnail displayed, click image for full size.
crash msg
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Bombastus !RZEwn1AX62!!xXxJO70U - Wed, 22 Jun 2016 20:35:15 EST V1Ngvki3 No.77997 Reply
>>77991
Chemdraw + DFT = all you need for molecular analysis.
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Bombastus !RZEwn1AX62!!xXxJO70U - Thu, 23 Jun 2016 02:55:42 EST LtWIDIP2 No.78000 Reply
>>77999
Lol, nah. The second link on Google:
Density functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases.
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PotatoSamurai !/sly9iFJgg - Thu, 23 Jun 2016 12:19:24 EST H8Fdbu5S No.78001 Reply
I got a copy of it offa iptorrents, if anyone's interested.

Also, thanks
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Bombastus !RZEwn1AX62!!xXxJO70U - Thu, 23 Jun 2016 12:42:06 EST VlgIm71t No.78002 Reply
>>78001
Yeah, post the torrent if you can. I can't run DFT calculations at home so it'll be helpful.

They also show electron density and therefore electronic-reaction-based probability of "where-x- will react on this molecule".
If you can, run the DFT calculation for fluorobenzene. Then do a HOMO LUMO calculation. You'll see the elctron distribution on meta vs ortho/para and it shows you how it directs 90% para unlike other ortho-para reactions.

The only problem is that for molecules bigger than C10, it takes fucking 8 hours to run. Also a shitload of computing space
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PotatoSamurai !/sly9iFJgg - Fri, 01 Jul 2016 19:04:36 EST H8Fdbu5S No.78054 Reply
1467414276698.png -(147519B / 144.06KB, 1042x752) Thumbnail displayed, click image for full size.
I finally figured out how to sim things like decomposition temp and bond breaking/reforming. This is fuckin' awesome.
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Bombastus !RZEwn1AX62!!xXxJO70U - Fri, 01 Jul 2016 20:50:35 EST +JCbsCsc No.78058 Reply
>>78003
It requires a login. ):
How do?
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Thomas Turveydock - Fri, 02 Sep 2016 21:04:30 EST BClNdd0H No.78211 Reply
>>78002
>it takes fucking 8 hours to run. Also a shitload of computing space
Could you elaborate on what computing resources it takes/what gives you the most mileage? I'm buying a new laptop soon and would like to start playing with frontier orbitals, docking, ADME modeling, etc.

If a decent graphics card can speed these computations, that's a real plus.
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Bombastus !uYErosQbLM!!Mybq1UbK - Sat, 03 Sep 2016 17:34:10 EST Req4jw5M No.78217 Reply
>>78211
I'm absolutely computer inept.
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trypto - Tue, 06 Sep 2016 16:52:28 EST 6/EmvHqc No.78221 Reply
>>78211
I'm not too familiar with molecular modelling, but I know it uses similar computations as neural networks. That is, it's mostly linear algebra, and having a good graphics card is very useful. In the NN world, an NVIDIA chipset will get you much further because it understands CUDA instructions. On the other hand, AMD chipsets use OpenCL, which is less supported. Last time I tried out modelling software (5 years ago), this was also the case. So I would look for a laptop with NVIDIA graphics... Except I've also read bad reviews about NVIDIA shit in laptops. Maybe that's old, or linux-specific, but be sure to check out reviews.


I sincerely doubt you'll be able to do any modelling on a laptop under $3k. On the other hand, you could probably build a PC with a lower midrange graphics card for $600 that could outperform the $3k laptop.
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Clara Cremmerkedge - Sun, 09 Oct 2016 21:50:55 EST mC4q4Hy7 No.78278 Reply
1476064255773.jpg -(58482B / 57.11KB, 401x500) Thumbnail displayed, click image for full size.
DICKS EVERYWHERE

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