Explicitly heating your protein
Tricky thing, heating up a protein. I’ve been playing around with GROMACS and have gotten to the point that I want to set up a simulation of a protein in a periodic box of waters somewhat carefully. That means that I have to slowly heat up a system. Here, I’ve followed the standard procedure of applying thermostats in increasing 50K chunks. This following video shows a 30ps simulation where each 5ps is run at an increasing hotter chunk of 50K. I really couldn’t be fucked putting positional constraints on the protein:
The result is rather hypnotic as the water goes from a wobbly jelly to an swarm of angry molecules. However, these waters are rather unphysical since below ~250K, the water really should be frozen in any number of crystal states. I’ll leave this for the force-field mavens to explain.
