GROMACS version:2023.3
GROMACS modification: Yes/No
Let’s consider a room packed with people, leaving no room for movement. If I want to stretch my hands, I require some space; thus, removing one or two people from the room or expanding room size becomes necessary to accommodate the stretching.
Similarly, within a box brimming with lipids (representing other people), how can a protein undergo conformational changes (similar to stretching hands) if no lipids are removed from the box? The solution lies in either removing some lipids or expanding the box size. Without creating additional space or adjusting the environment, the protein would struggle to achieve its desired conformational alterations within the confined space.
So what is the solution for above condition?
Dear @jalemkul , any insights will be greatly appreciated. Thanks