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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
