How to Perform FEP Analysis in GROMACS?

zako · 发表于 Post on 2025-7-25 07:43:07

Hello everyone,
I want to perform Free Energy Perturbation (FEP) analysis using GROMACS, especially for comparing two similar ligands (eg one atom difference).
Can someone please outline the basic steps?
*How to prepare the system for two states (A and B)?
*How to set up .mdp files with lambda values?
*Do I need other tools ?

Any tutorials, scripts, or advice would be really helpful. Thanks!

greatzdk · 发表于 Post on 2025-7-25 14:38:29

Try this code. https://github.com/luancarvalhomartins/PyAutoFEP

greatzdk · 发表于 Post on 2025-7-28 10:07:30

and this https://github.com/yiqichenshallwetalk/FEP-on-GPU-Workflow

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