Judging Convergence on Free Energy Calculations

From: Ethan Croitoru (ecroitoru1_at_gmail.com)
Date: Fri Jan 15 2021 - 13:45:40 CST


I am trying to run free energy calculations on a transmembrane helical
dimer. I have been trying to closely follow the protein ligand tutorial to
do these calculations (
I have a question about judging convergence of the PMFs. Taking the bound
conformation calculation as an example, using the RMSD colvar, could one
look at the protein's rmsd plateauing as a sign that the PMFs are also
converging. Or should I be looking for my PMF values to also be plateauing?
In a similar vein, around how many steps should convergence be happening

Thank you for the help,
Ethan Croitoru

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST