[gmx-users] Protein-ligand system simulations with GROMACS

[Guillem Prats Ejarque]

Dear colleagues,

I'm starting to use GROMACS and I'm simulating a system between an RNA binding protein and a small RNA ligand (a dinucleotide, ~60 atoms) in a cubic box. I set  AMBER99SB-ILDN protein, nucleic AMBER94 as a forcefield, with a tip3p water model.

This was only to put you in context. My question is, which parameters should I take into account with my system during the production run? Which should be the duration of the run? And what about the equilibration?

Thanks a lot for your attention,

Guillem