When I look at the videos that show molecular dynamic simulations, I wonder if the motion speed that we see corresponds to real time or if it is slowed down for display.

Definitely slowed down for display.

Our videos normally are of about 50-100 nanoseconds simulated time. But you see them in few seconds and or minutes at a frame rate of 20-25 fps. Each frame of the video is about 0.1 nanosecond. Therefore you are seeing around 2 nanoseconds of simulation per second (real life).

Hope that answers your doubts.

cheers,
i

Thanks for your answer ignasi. The slow down factor of 500 Million times is enormous. I would have expected some slow motion but not with such a huge factor. At nanoscale we have also nanotimes. Maybe it is a logical scaling for nature:

Meters -----------------> Seconds
Millimeters -----------> Milliseconds
Micrometers ---------> Microseconds
Nanometers ---------> Nanoseconds