View this post on Hive: Particle in a Double well potential: A molecular dynamics toy example using openMM toolkit
Particle in a Double well potential: A molecular dynamics toy example using openMM toolkit
6 years ago by dexterdev (62)
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The animated title pic really does a fantastic job of drawing the viewer in. I'll have to try that at some point. Also, very cool introduction to Brownian motion and how coding can help analyze this phenomena.
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This reminds me of a very simple atomic model I produced at school. That was many years ago and the computers were not up to what can be done now.
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Wow, and I thought I worked hard on my posts :D
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:P I have to improve a lot though.
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I don't know if you have to, but everyone can and progress is in big part what life is about I think. :)
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Oooo my God...... Interesting things there in your blog and for so many years I never really met most of the things in said in your blog, which simply means, am really educated today. And I enjoyed the class even though I didn't pay an tuition..... Lol
Lovely work in there and every time spent on your blog was really worth it. Great pictures too.
Great work and keep the science and technology spirit up
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😃
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Cool
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Wow, very nice. But I have to admit I have to read your other publications as well to get further into this subject. Where are these two minima from again? Don't get it!
Regards
Chapper
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Hi @chappertron : Thank you for stopping by :) So the minimas are embedded in the potential function which I defined in the beginning.
This is how the function is:
You can see that there are 2 minimas at X=1 and X=-1 in this function.
See this plot(@ Y=0):
You saw the 2 minimas? Our particle toggles between these 2 states.
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Oh of course! I have to look closer next time. Reminds me of my biophysics courses at the University used to.
So this equation would explain why the yellow dot moves as it moves in a crowd of smaller particles?
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No. If the yellow particle was allowed to move freely, Potential surface would be like a flat plane surface. But now if I compel my particle under this curvy potential with two minimas, that is what I am defining by this equation. Great question btw. I should have been more clear in the article. But I hope people read comment section too. :)
By the way, just defining this potential function won't make things alive. That's what the langevin equation is there. That equation gives life to the particle under whatever potential you define.
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Very cool reply!
The langevin equation makes things become alive
That's mathematics at it's best.
Thanks again
Best
Chapper
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The animated title pic really does a fantastic job of drawing the viewer in. I'll have to try that at some point. Also, very cool introduction to Brownian motion and how coding can help analyze this phenomena.
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