From: Ethan Croitoru (ecroitoru1_at_gmail.com)
Date: Fri Jan 15 2021 - 13:45:40 CST
Hi,
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 (
http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf).
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
around.
Thank you for the help,
Ethan Croitoru
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