I want to do a simulation of an atom (type atom is not important) bouncing inside a spherical surface (the material of the surface is not important too) (i.e. starting from an initial velocity, the atom upon colliding with the spherical shell, continues moving and bouncing, etc.). I am totally new in molecular simulation. What must I learn for do this? Thanks.

  • $\begingroup$ Just to confirm, are you really interested in an atomic simulation or mainly some property of this idealized scenario (particle constrained to move within a sphere)? In the former case, you will want to learn the basics of molecular dynamics and develop specific settings to model an atom in a sphere; while you might not care about what atom or what material the sphere is made of, these will both have a significant affect on the result of your simulation (e.g. will the atom burst through or bind to the surface). If it's the latter, mixing in actual atoms will complicate things significantly. $\endgroup$
    – Tyberius
    Dec 28, 2023 at 0:30
  • $\begingroup$ I want much less than that. Let's say I want the sphere to be made of carbon atoms and the atom that collided, too. (I don't even know what program is used for this haha). That's why I ask the question (I'm totally starting from scratch). I want to be able to know what scientific program is involved and be able to visualize what I want in three dimensions. That's all. $\endgroup$
    – eraldcoil
    Dec 28, 2023 at 0:32
  • $\begingroup$ And do you want to calculate something about the internal atom's trajectory or essentially just make an animation of the atom moving? $\endgroup$
    – Tyberius
    Dec 28, 2023 at 0:34
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    $\begingroup$ I'm not super well versed in how to set up the input for various MD programs, but this prior question will give some sense of the programs/software that is used for MD: mattermodeling.stackexchange.com/q/1215/7 I suspect someone on the site will eventually be able to provide a more detailed answer for you, but just note activity tends to be a bit lower around the end of the year, so it may be awhile before users with the right expertise and time on their hands see your question. $\endgroup$
    – Tyberius
    Dec 28, 2023 at 0:41
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    $\begingroup$ If you know enough about programming, you can write a code that can do this for you. Graduate students (in many courses) routinely write a toy MD code that can do simulations of liquid argon (it will only have LJ interactions and is fairly easy to code). $\endgroup$ Feb 17 at 19:30


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