Clarifications on documentation for thermostatting with partial temperature

Disregard this topic.

For such a tiny system you cannot talk about “Temperature” in a meaningful way.

You’re right. I meant to say some arbitrary number, like 3000 maybe. I just wanted to get a better general understanding of what is going on behind the scenes.

Please set up a meaningful example system (try ~30000 atoms), apply the commands you think you should, and observe yourself. And only then you should ask about specific details that don’t match your expectations.

More generally speaking, any question about MD simulations that starts with “let’s suppose” still has so many open degrees of freedom where things could be implemented slightly different or people make different assumptions, that it can only lead down a deep rabbit hole and quickly become a wasted effort.