system
Given the following post, respond as if you're commenting on Reddit:
human
In Molecule Dynamics modelling, why are calculations initiated at 0K and slowly heated to the desired temperature, rather than initiating at 300K immediately?

I've been reading papers on mechanism studies of various enzymes.

In these papers, they start at 0K and slowly heat it to 200K, then hold, then slowly heat 300K again in their computational software.

Why is this?
gpt
I do MD for a living, and this is mostly a historical artifact. In the old days, the starting structures weren't typically very good. So even with the help of a thermostat, errors introduced by the crystallographic modeling process could be a high enough energy locally that it could lead to an unstable system. But nowadays with better starting structures, you can usually get away with minimizing your system a bit and reinitializing temperatures at your desired temperature.

However, for some research groups that have been around long enough, they still do it the old way. It's not wrong, it's just inefficient.