An Introduction to Molecular Dynamics

แชร์
ฝัง
  • เผยแพร่เมื่อ 23 ธ.ค. 2024

ความคิดเห็น •

  • @rhysknight8681
    @rhysknight8681 3 ปีที่แล้ว +2

    Great explanation Thunderf00t I was half expecting you to start telling me why atoms were bullshit

  • @imnotnia
    @imnotnia 10 ปีที่แล้ว +38

    Thunderf00t?

  • @behnamasid
    @behnamasid 11 ปีที่แล้ว +10

    Is this Thunderf00t? amazing video mate

  • @jony7779
    @jony7779 9 ปีที่แล้ว +22

    thunderfoot is that u?

  • @AleaTeo
    @AleaTeo 3 ปีที่แล้ว

    Can you please tell me what's he saing from 0:06 to 0:09, I don't get it. I mean I don't get why he concludes that "it means that they come out has hard spheres". Thanks

    • @mazin627
      @mazin627 20 วันที่ผ่านมา

      Using LJ potential means that the atoms cannot overlap and hence approximate a hard sphere model.

  • @jorgejimenez4325
    @jorgejimenez4325 2 ปีที่แล้ว +1

    Bro wtf its thunderf00t. I'm in biochem in the year 2022. flash back boys

  • @wertytrewqa
    @wertytrewqa 5 ปีที่แล้ว +5

    thanks thunderf00t. u made this simple to understand

  • @ranam
    @ranam 5 ปีที่แล้ว

    Can I simulate hydrogen plus oxygen gives water products to reactants with only telling number of Hydrogen atoms and oxygen atoms where the equations satisfy scrodinger equation so the reactants will give this product for checking every chemical equations without memorizing the equations please tell me if IAM wrong simply can I check the chemical equations even the sulphuric acid preparation reactions or uranium reactions or just combine two atoms and can I tell their products

  • @amitimsc
    @amitimsc 4 ปีที่แล้ว +2

    Garbage in garbage out! Heard the term after many years :) Thank you.

  • @essentialsofbiology1643
    @essentialsofbiology1643 5 ปีที่แล้ว

    Beautiful! Just one question - I couldn't make out the words at 0:06 - 'and what with the six twelve potentials typically used to represent such things?'

    • @nomadsland7195
      @nomadsland7195 4 ปีที่แล้ว

      Isn't he talking about the Lennard Jones potential ?

  • @willch7481
    @willch7481 6 ปีที่แล้ว +1

    which software do u recommend for molecular dynamics simulations?

  • @egs8545
    @egs8545 3 ปีที่แล้ว +1

    can anyone tell me the maximum length of time achievable for an MD run?

  • @InfiniteUniverse88
    @InfiniteUniverse88 5 ปีที่แล้ว

    Do these models take steric hindrance into account?

  • @aeroscience9834
    @aeroscience9834 4 ปีที่แล้ว

    Did thunder00t take this video down or something?

  • @drnosy
    @drnosy 6 ปีที่แล้ว

    Hi! Can someone explain what the axes are for plot at 1:32? Thanks!

    • @BioAnimationsForMe
      @BioAnimationsForMe 6 ปีที่แล้ว +2

      I would suppose that the x-axis is Å (10^-10 meters) and y-axis is probability of an oxygen being found at that distance from a water molecule, normalized to the average. It suggests there is structure to water; a water molecule quite frequently has oxygen atoms at a distance of 3 Å from it.

  • @bonbonpony
    @bonbonpony 3 ปีที่แล้ว +2

    So how do you calculate the interactions between charged particles when there's so many of them? I'm pretty sure that calculating the attraction/repulsion between each pair of particles would be _extremely_ inefficient. Are there any better ways of doing that?

    • @eriknordquist
      @eriknordquist 2 ปีที่แล้ว +1

      You're right that it would be extremely inefficient to treat each pair explicitly, although on a good graphics card, these kinds of simple computations can be done much more efficiently in parallel. But for a serial calculation, the clever trick performed is to use a cut-off distance. Before that distance, the pairs are calculated explicitly. Beyond it, they are smoothly switched to zero. The van der waals interactions decay as r^(-6), and are usually ok to switch off after 1-2 nanometers, or more than 10x the length of a chemical bond. With cutoffs, the efficiency of a simulation scales linearly with the system size; without cutoffs, it scales quadratically.

    • @eriknordquist
      @eriknordquist 2 ปีที่แล้ว +1

      Oh I just remembered something else! There is a loss of information if you cutoff too soon, which happens for interactions between charged bodies using the pair-wise 'electrostatic' interaction, or Coulomb's Law which goes as r^-1. It's a bit hard to defend WHY in the comments section, but believe me that this decay is too gradual to every properly cut-off. "Everything in the universe is both gravitationally and electrostatically coupled." The clever trick that saves us this time is called a Fast Fourier Transform. Definitely beyond my ability to explain in person or in a comments section. en.wikipedia.org/wiki/Ewald_summation en.wikipedia.org/wiki/Fast_Fourier_transform

    • @bonbonpony
      @bonbonpony 2 ปีที่แล้ว +1

      @@eriknordquist Don't worry, in my country there's a saying that pretty much translates to English as: "For a smart head, a word is enough". So all you need to do is name it, and I can find all the details myself. I'm well accustomed with FFT, so there's that, I just don't know how can this be used for calculating interactions between particles. One possibility that comes to my mind, is something similar to Taylor series approximation (which Fourier transform actually is too, since it can be represented as a complex power series): approximating the "shape" of the potential in space with lower-frequency harmonic functions where a rough approximation is OK, and adding more components where we need it more detailed.
      But since you mentioned the "cut off distance", there's one more thing that occurred to me: Maybe we could use Gauss's Law here in some way for those electric potentials? (it should also work for gravitation) I remember that Newton had a similar problem when he tried to calculate the gravitational attraction betwen the Earth and the Moon, and it turned out that he would have to calculate attraction between every atom of the Earth and every atom of the Moon, which would require him to calculate a six-fold integral! :q
      But then Gauss came in later and showed that this heinous calculation can be replaced with a simpler one (a surface integral), because you can draw an imaginary surface (a bubble) around some mass or charge density, and the gravitational attraction or electric force on its surface would be proportional to the mass or charge density enclosed inside the bubble.
      Which gave me an idea: Perhaps we could draw such imaginary bubbles around groups of particles and store them in a tree-like structure for faster sorting, so that when our test particle is outside a particular bubble, we wouldn't have to calculate attraction from all the bubbles inside, but they could be replaced by their common "center of mass" (or "center of charge in this case"), thanks to Gauss's law? :>

  • @science_10523
    @science_10523 7 ปีที่แล้ว

    i am using orca for QM calculations. but not able to do the MM part. is there any tutorial video for open source QM/MM interface? can anyone give any suggestion.

  • @science_10523
    @science_10523 7 ปีที่แล้ว +1

    nice explanation. the simplest way to define MD simulation.

  • @hulusicengiz9725
    @hulusicengiz9725 6 ปีที่แล้ว +1

    Hello there, these sources are great and thanks for sharing with us. I need to ask you something about molecular dynamics simulations which is showing in this video which program was used to create? I try to use Matlab simulation as you know that has a lot of option. Can you suggest me to use which program for this? Thanks for interesting.

    • @blacknoir2404
      @blacknoir2404 ปีที่แล้ว

      That is the question of the century. Maybe they’ll come out with a decent molecular dynamics simulator and put it on steam, similar to what was done with universe sandbox.

  • @omarbarghouth5429
    @omarbarghouth5429 6 ปีที่แล้ว

    i have some questions about molecular simulation, can you answer me please ?

  • @עדיבריל
    @עדיבריל 5 ปีที่แล้ว

    hi, i would like to use a small part of this video for a project i am working on.
    is there a way i could purchase a licence to use it?

  • @Marmots4reFun
    @Marmots4reFun 4 ปีที่แล้ว

    Sorry for the very basic question, but would this method be used to predict the 3-D structure of a glycoprotein if you knew the amino acid sequence and the structure of the attached glycans?

    • @peterlauridsen8403
      @peterlauridsen8403 11 หลายเดือนก่อน

      You would need ab initio homology/structural modeling for that. Something AlfaFold readily provides these days

  • @jersonantigua9885
    @jersonantigua9885 6 ปีที่แล้ว

    can someone help me interpret my docking results?

  • @cyrusIIIII
    @cyrusIIIII 8 ปีที่แล้ว +2

    What software is this?

    • @galvanizedcorpse
      @galvanizedcorpse 8 ปีที่แล้ว +1

      for MD simulations I use GroMaCS, and for some other 3D animations in the video you can start with blender, both are free, but gromacs runs only in Linux

    • @cyrusIIIII
      @cyrusIIIII 8 ปีที่แล้ว

      Гальванизированный Труп Is it for Chemistry students or biology?

    • @Lexoka
      @Lexoka 6 ปีที่แล้ว

      @cory Gromacs is definitely for molecular simulations, but Blender indeed is not.

  • @bonbonpony
    @bonbonpony 9 ปีที่แล้ว

    How do you make those simulations in your video? Is there some clever way to simulate all these atoms interacting with each other without explosion of computations?

    • @gelatinocyte6270
      @gelatinocyte6270 4 ปีที่แล้ว +1

      Some simulation videos are actually timelapses sometimes. MD simulations don't really make your computer explode; it only takes mathematical calculations (which are what computers are made for anyway). It's just that it strains the computer the more variables you add to it that in needs to account for. Think of it as having to take the same simple test over millions of times in quick succession - that's stressful!

    • @bonbonpony
      @bonbonpony 4 ปีที่แล้ว

      @@gelatinocyte6270 I know how computer simulations work. By "explode" I didn't mean the computer to explode, but the number of calculations to grow exponentially with every new element you add to your simulations, because the number of interactions between particles grows as well. I was rather asking about what software do they use to render such simulations and what rendering techniques do they use so that the end results look so good.

    • @eriknordquist
      @eriknordquist 2 ปีที่แล้ว +3

      @@bonbonpony I didn't make the video, but I feel I can answer your question. There are several major simulation packages for serious simulations of biological systems, by far the most common in academic research are charmm, amber, and gromacs. Of these, gromacs is the easiest to play with without previous experience. Amber is probably fastest, and charmm is most powerful/flexible. I think gromacs can have a GUI, amber and charmm do not. You had a question about efficiency before, so I'll mention a fourth package called Desmond, which is specially written for a supercomputer called ANTON. In fact, desmond and Anton were literally made for one another, meaning they were designed together to optimize efficiency of parallel computing-- avoid the "explosions" you're rightly worried about. On Anton, a simulation that might run for weeks on a computer with a GPU, or months on a single processor, will take only MINUTES (an amazing, true fact that kind of makes me smile :). To render the movies, you can use a software called VMD, visual molecular dynamics. Both gromacs and VMD are free.

  • @19neetish
    @19neetish 9 ปีที่แล้ว +1

    I want to do some MD simulation for interaction of surfactant and nanoparticle at oil and gas water interface. I am pretty new to this field. Can any one suggest where to start.

    • @ryuuzaki24
      @ryuuzaki24 8 ปีที่แล้ว

      dunno if you are still interested in doing that but gromacs has amazing tutorials to simuations including 2phase interactions

    • @19neetish
      @19neetish 8 ปีที่แล้ว

      ok

  • @mochipickles
    @mochipickles 2 ปีที่แล้ว

    Absolutely beautiful

  • @r.i.p.volodya
    @r.i.p.volodya 4 หลายเดือนก่อน

    Thank you - a very useful overview.

  • @dianaouk9232
    @dianaouk9232 ปีที่แล้ว

    I giggle at the water jiggle @0:57

  • @jojomclan4323
    @jojomclan4323 11 ปีที่แล้ว

    wow its very fascinating thank you.. i hope i can find more of these videos on MD

  • @Novak2611
    @Novak2611 11 ปีที่แล้ว +2

    That's wonderful!!!

  • @dr.rameshbhise2178
    @dr.rameshbhise2178 4 ปีที่แล้ว

    Excellent presentation. Thanks a lot!

  • @gayatriprasad3790
    @gayatriprasad3790 4 ปีที่แล้ว

    Good video presentation.

  • @Hurrdurrderpable
    @Hurrdurrderpable 6 ปีที่แล้ว +1

    suddenly a wild thunderfoot appeared

  • @lt.arvinddhurve626
    @lt.arvinddhurve626 4 ปีที่แล้ว

    amazing video

  • @jayashreebagawade696
    @jayashreebagawade696 4 ปีที่แล้ว

    Thank you for informative lecture.

  • @WeallMaharashtra
    @WeallMaharashtra 4 ปีที่แล้ว

    Nice explanation

  • @hemantkumarmeshram7304
    @hemantkumarmeshram7304 4 ปีที่แล้ว

    Interesting video.

  • @drbinus1064
    @drbinus1064 4 ปีที่แล้ว

    Very informative session.

  • @universaleducationpoint4605
    @universaleducationpoint4605 4 ปีที่แล้ว

    Nice

  • @idegteke
    @idegteke 10 หลายเดือนก่อน

    You somehow always are expected to assume that every phenomenon can only contain the amount of intricacy (depth, information) its investigated interactions with matter (atoms) or energy (waves) let us to consistently measure, perceive and discover. Never hypnotizing any further “weird” parameters or entities has become the norm of being smart or at least not being an idiot. Well, until you have enough proven scientific knowledge to automatically get that privilege of idiocy - given you can relate your unquestionable ultimate existing knowledge and your arbitrary idiocy.

  • @surajitmandal8225
    @surajitmandal8225 4 ปีที่แล้ว

    Awesome.

  • @rsphysics2646
    @rsphysics2646 4 ปีที่แล้ว

    Thank you

  • @mehuldave6839
    @mehuldave6839 4 ปีที่แล้ว

    Superb!

  • @dr.rajeevamp3487
    @dr.rajeevamp3487 4 ปีที่แล้ว

    Nice one Thank you

  • @nagabhushanabr8479
    @nagabhushanabr8479 4 ปีที่แล้ว

    Thanks

  • @jlpsinde
    @jlpsinde 6 หลายเดือนก่อน

    COOL

  • @1NazareeM618
    @1NazareeM618 11 ปีที่แล้ว +1

    i see why nano tech is so infinite and dangerous and probably exterme Fun when u have the tech and lab to practice it ...and i can see why nanomites could be a real threat..u can play God with that tech ..and thats what the most powerfull are doing i suppose ..

  • @jamesmcginn6291
    @jamesmcginn6291 6 ปีที่แล้ว

    An "okay" job simulating water. Obviously your theory is wrong. This is what you don't have right:
    Do a search for "paulings omission" James McGinn Incidental Symmetry

  • @GabbyTwange
    @GabbyTwange 7 หลายเดือนก่อน

    You and fer laqafxae. Poinca

  • @EternalSearcher
    @EternalSearcher 11 ปีที่แล้ว +2

    Neeeeerdy. I bet narrator doesn't even have a girlfriend.

  • @cultofsogga5863
    @cultofsogga5863 4 ปีที่แล้ว +1

    Awful! Speaker.

  • @dr.lathan7263
    @dr.lathan7263 4 ปีที่แล้ว

    Nice