Oil and water separation by molecular dynamics simulation
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- Опубликовано: 13 янв 2013
- Molecular dynamics simulation of oil (pentane, C5H12) and water separation at 300 K temperature and 1 atm pressure.
List of my MD simulation videos: / mdsimulator 
Наука
When you find the password to your university’s super computer:
Usually some are open for students but for homework and coursework only 😂
How long did it take to compute? on what system
Would this simulation be more of an emulsification representation as the oil is aggregating to form a sphere/micelle like structure? like if it was separation there wouldn't be complete surrounding of the oil droplet would there? please correct me if I'm wrong :)
Can I use your video for educational purpose? Thanks.
Hi guys, is it possible to simulate the bioabsorption process by GROMACS or any other MDS apps? it's necessary. Thx
Is this demonstrating clathrate hydrate formation?
I am intrigued. how did you do it? Can it be done in AMBER or GROMACS? if you have details please?
Which Force field did you use?
wow, it took less than 1 ns, so quick~
teacher how we can conform that the system is equilibrated (from which parameters we can conform aboute the structure is in the stable state) thank you teacher
what software do you use for this simulation? thnks
after 10 years, still no answer . . .
Hi professor. I'm currently and undergrad Biochemistry student. What is the computational requirement to simulate a cell or even an organ down to the atomic level? How long will it take to render a few seconds animation on a modern super computer? And on a quantum computer? Thank you.
Probably just 24 of the desktop computers in my computer lab (they are like super fast with graphics and computing) could all do an entire cell. But seriously dude, thats a question for Quora.com
i don't think you could simulate a complete cell atomistic model with current computational machine xd, i simulate 700000 atoms model with most powerful GPU (tesla v100) and 40 CPUs, and it runs 0.5ns simulation-time/day.
But the number of atoms in a cell is 100,000,000,000,000 hahaha...not even talk about a organ, btw the computation time of MD is O2. That is why we usually simulate just a little part of cell, like a hole on the membrane, ligand and enzyme.
@@user-lr4rp5ch2e what If we use Quantum computer And AI
Dev do futuro I don’t really know the capability of quantum computer, so I cannot answer you this question.
About AI, some people use the AI technique to obtain the meso-scale property of the granular particle, so when they try to simulate the whole cell, the component is no longer atoms but those granular particles, and it reduces lots of computation. I am not sure wether we can call it MD or not, but if you say “can we simulate a cell with particle method?” The answer is yes and just like i mention above. I’ve seen a researcher in APCOM2019 mini symposia who simulates a cell behavior by that.
@@user-lr4rp5ch2e thanks for the answer. Have you seen Google AlphaFold? Can It help in This process? ruclips.net/video/GQH-zWUylPY/видео.html
How Can i get parameters of oil
Does anyone know the name of this song?
I need to know asap.
Why is Water Shaped Like That?
A water molecule has only three atoms, so intuitively it should have a linear shape. But because oxygen has free electrons, and the electric charge makes the electrons avoid each other, the molecule shape has to be in a configuration that tries to maximize their distance. So it gives it a bent shape. However, if you are wondering why it doesn't have a spherical shape, that's because it doesn't really affect the simulation.
What I'm wondering is why, sometimes, the oil molecules seem to dissapear/teleport.
This simulation is set in such a way that, when a molecule leaves the box at one side, it enters the box on the opposite side. This is called a 'periodic boundary condition'. It's a trick for simulating large systems
+Cystlib DFT? Ab initio? using planewave basis?
+Yonoodle Hsieh I don't think any quantum mechanical based methods are being in this simulation but instead a force field is being used
@@Cystlib Nice. PBC looks much more weird when the molecule being simulated is larger than the box, like protein molecules. At times its almost hilarious.
Hey guys, I am chemistry undergrad and I want to learn all of this. From the very beginning to possibly simulating cell walls and $hit.
Can anyone help me please. Like I don't even have a clue where to begin with ? What is all this DFT Force field Ab initio Amber etc. etc. 😭....
I have pretty good computer. And I wish I knew all this so that I can simulate molecules and reactions, instead of playing games in it.
Please can anyone help, where should I begin, how should I begin, I want to be learned like you all guys are in this field.
Thanks ❤
XD
FUUUCK THIS SONG'S A WOBBLER