From: alli suliat (alliadeola17_at_gmail.com)
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
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?
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