GROMACS version: 2025.4-conda_forge
GROMACS modification: No
Hello, I am wondering what are standard publishable preprocessing workflows for AlphaFold3-predicted complex structures to prepare them for GROMACS MD simulations?
I would like to carry out molecular dynamics (MD) simulations on protein complex structures predicted by AlphaFold 3, and I understand the raw predicted structures cannot be directly used for simulation. Could anyone share the standard, publication-grade structural preprocessing workflows to refine and convert these AlphaFold3 models into valid, production-ready starting structures for GROMACS-based MD simulations? I am eager to learn the detailed routine steps and key considerations for this structural preparation stage.
I am working on a complex of protein and DNA (cause they both do not have a experimental structure, so i have to use alphafold3 prediction)