FEL to find starting structure for SMD

User discussions
1

GROMACS version: 2024
GROMACS modification: No

Hello everyone,

I performed a 100 ns protein-ligand simulation of my system. My question now is which structure to use as the starting point of my SMD. My original ideas were either the starting position after minimization and equilibration, or the representative structure of the biggest cluster of conformations. However, I also calculated the Free Energy Landscape by calculating the covariance matrix and doing PCA. I then used the first and second eigenvectors to calculate the FEL and was able to extract the structure that represented the global minima of the FEL.

Would this structure be a reasonable starting point for the SMD, being the more stable conformation of the system? Am I understanding this correctly?

Thanks for your help!

2

clustering or FEL both are fine. I would go with FEL based on PCs

3

Thanks for the reply! Used the minima of the FEL