# Help understanding HADDOCK's different refinement methods
**URL:** https://ask.bioexcel.eu/t/help-understanding-haddocks-different-refinement-methods/5924
**Category:** HADDOCK
**Created:** [October 29, 2025, 8:24pm UTC](https://ask.bioexcel.eu/t/help-understanding-haddocks-different-refinement-methods/5924 "2025-10-29T20:24:57Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@sgaray](https://ask.bioexcel.eu/u/sgaray)
#### Post date: [October 29, 2025, 8:24pm UTC](https://ask.bioexcel.eu/t/help-understanding-haddocks-different-refinement-methods/5924/1 "2025-10-29T20:24:57Z")
Hi all. I got this result from AlphaFold2 for a heterotrimer, and I want to check out different binding options using the ‘refinement’ method. I see the interface gives me four different choices: ‘water refinement (default)’, ‘coarse grained refinement’, ‘energy minimization refinement’, and ‘simulated annealing with centroid restraint’.
I tried the water refinement and it gave me a bunch of useful binding alternatives, but the ‘simulated annealing with centroid restraint’ option only gave me back a single structure.
Could someone give me some info about this ‘refinement’ method? I’ll take any information I can get. Thanks!
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 30, 2025, 10:28am UTC](https://ask.bioexcel.eu/t/help-understanding-haddocks-different-refinement-methods/5924/2 "2025-10-30T10:28:52Z")
If you just want to refine your complex, the default protocol is best.
It does perform a very short MD in water and does generate several models.
For more details of the various protocols (in the context of refining low/medium resolution EM models) check the following paper:
- T Neijenhuis, S.C. van Keulen and A.M.J.J. Bonvin. [Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4](https://doi.org/10.1016/j.str.2022.02.001). _Structure_ _30_, 476-484 (2022).
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### Author:  [@sgaray](https://ask.bioexcel.eu/u/sgaray)
#### Post date: [October 30, 2025, 10:09pm UTC](https://ask.bioexcel.eu/t/help-understanding-haddocks-different-refinement-methods/5924/3 "2025-10-30T22:09:25Z")
Thank you very much Dr. Bonvin!