**From:** Ethan Croitoru (*ecroitoru1_at_gmail.com*)

**Date:** Fri Jan 15 2021 - 13:45:40 CST

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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

**Next message:**Josh Vermaas: "Re: Judging Convergence on Free Energy Calculations"**Previous message:**Paula Mihaljevic-Juric: "FATAL ERROR: patch has 127043 atoms, maximum allowed is 65535"**Next in thread:**Josh Vermaas: "Re: Judging Convergence on Free Energy Calculations"**Reply:**Josh Vermaas: "Re: Judging Convergence on Free Energy Calculations"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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