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I'm not sure if this is the right site to ask a such question. But I'm getting to learn the world of the small.

I know there is software out there like NAMD, and LAMMPS. But these tools are very non-intuitive, having complex interfaces that seem to hide the underlying mechanics.

I'm looking for something that can display live molecular simulations in 3D, with some kind of inbuilt editor to simply place, or remove atoms.

Again, sorry if this is the wrong place for a such question, I'm sure from what you can tell, I am extraordinarily new to this area of knowledge. I would greatly appreciate any feedback. I fear although, I will have to create my own intuitive frontend to NAMD or equivalents to have essentially a 'quantum sandbox'

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  • $\begingroup$ Albeit not as complete as other packages can be, Ascalph is what you describe biomolecular-modeling.com/Ascalaph/index.html $\endgroup$ – The_Vinz Dec 1 '19 at 22:19
  • $\begingroup$ Also: I have not tried it myself, but it should be possible to set up VMD so that it "streams" the output of MD packages like LAMMPS $\endgroup$ – The_Vinz Dec 1 '19 at 22:33
  • $\begingroup$ I strongly recommend openmm. It is the easiest of the packages to interact with, followed by LAMMPS. I believe Macsimus also has video options, but I have never used it $\endgroup$ – B. Kelly Dec 2 '19 at 1:01
  • $\begingroup$ Avogadro has a live minimizer when editing - pulling, adding, deleting atoms, changing bond orders, etc. The next version (v2) will support full MD. $\endgroup$ – Geoff Hutchison Dec 5 '19 at 16:34
  • $\begingroup$ Since this question has been up for a couple weeks and still doesn't have an answer, perhaps it might be something that a dedicated computational chemical physics community would be interested in. There is a proposal for a Stack Exchange for Materials Modeling for example: area51.stackexchange.com/proposals/122958/…. Perhaps you might consider supporting it if you think it would be useful for you! there's already MD questions there. $\endgroup$ – user1271772 Dec 10 '19 at 3:12

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