Hi everyone,
I’m relatively new to GROMACS and I’ve been exploring its capabilities for simulating ligand-protein systems. I’ve mostly worked on protein-only simulations so far, but now I want to move into protein-ligand complexes (small molecules docked into active sites). I’m wondering:
- What are the best practices for setting up such systems in GROMACS?
- Are there any specific force fields or tools recommended for generating ligand topologies (besides PRODRG, which seems a bit outdated)?
- How do people usually validate or check the stability of such complexes over long simulations?
Would really appreciate any insights or shared experiences—especially any gotchas I should be aware of during preprocessing or production runs. Thanks in advance!