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

Guillem Prats Ejarque Guillem.Prats.Ejarque at uab.cat
Tue Feb 23 20:38:41 CET 2016

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,


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