Advice for Protein Mutation FEP Calculations

From: Matthew Guberman-Pfeffer (
Date: Tue Dec 01 2020 - 10:27:43 CST

Dear NAMD community,

I want to study how one or more residue mutations impact the stability of a
protein-protein complex. I've worked through the tutorial on alchemical
transformations, but I have some additional questions, and would appreciate
advice on how to set options that have since been implemented in NAMD.

1) Should I minimize/equilibrate the bound and unbound protein that will
undergo mutations before or after creating the hybrid topology? Does it

2) How do you choose the value of alchLambdaIDWS?

3) When is it appropriate to use alchWCA/alchRepLambdaEnd orc
alchBondLambdaEnd/alchBondDecouple. If so, again, how do you choose the
appropriate settings?

Best regards,

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