Free Energy Pertubation simulation set-up

From: alli suliat (
Date: Sun Dec 06 2020 - 18:19:23 CST

Dear NAMD Users,
I'm interested in obtaining in-silico binding affinities of some
protein-ligand complexes by using NAMD. I've looked over the alchemical
free energy perturbation tutorials with NAMD. However, I do not understand
how the simulation process works or how to set-up my system for the FEP
1) One has to set-up two separate systems of; A (protein plus ligand) and B
(ligand only)?
2) Can a previously minimized and equilibrated system be used for the
3) How long should the FEP simulation be?
4) How is the lambda state in the configuration file determined?
Thank you.

Adeola Alli

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