It's two separate things, both mentioned in your question: simulation then animation. Both steps are computationally expensive enough that they can't be done in one run.
For simulation, typically a molecular dynamics code is used along with features specific to biological analysis (since MD by itself is a physics simulator). NAMD is one of the well-known MD tools used for bio work. Depending on the complexity and features/accuracy sought, a whole host of other tools might be involved. The timeframe of simulation is of the order of weeks to months given massive computational power (e.g., a large allocation on one of the national supercomputing grids).
Once tons of simulation data is generated (as the output of simulation), then 3D visualization tools can be used. NAMD has a sister vis tool called VMD. Blender is another option. Incidentally, Janet Iwasa (the narrator and researcher behind this work) is a visualization expert, so it's likely she only worked on the second step (animation) by using existing simulation data, or collaborating with a simulation group. (Again the computation required for rendering is very high, on the order of days to weeks using a large allocation on a supercomputer).
Drew Berry creates similar animations and refers to them (in this talk) as "accurate representations", but doesn't go into much detail. Interesting history in the beginning as well. https://www.youtube.com/watch?v=WFCvkkDSfIU
Yes, that was my first thought as well. I'm curious what parts are accurate and what parts are simplifications for ease of visualization and comprehension. Colors are clearly not representative. What about movements? Relative speed of movements? Shapes? Density? If we could see these processes in some magical microscope would this look close to what is happening or not?
For simulation, typically a molecular dynamics code is used along with features specific to biological analysis (since MD by itself is a physics simulator). NAMD is one of the well-known MD tools used for bio work. Depending on the complexity and features/accuracy sought, a whole host of other tools might be involved. The timeframe of simulation is of the order of weeks to months given massive computational power (e.g., a large allocation on one of the national supercomputing grids).
Once tons of simulation data is generated (as the output of simulation), then 3D visualization tools can be used. NAMD has a sister vis tool called VMD. Blender is another option. Incidentally, Janet Iwasa (the narrator and researcher behind this work) is a visualization expert, so it's likely she only worked on the second step (animation) by using existing simulation data, or collaborating with a simulation group. (Again the computation required for rendering is very high, on the order of days to weeks using a large allocation on a supercomputer).