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

Dries Van Rompaey dries.vanrompaey at gmail.com
Tue Feb 23 20:50:16 CET 2016


These questions are quite specific to your problem. There's no way we can
predict what equilibration time will suffice for your system. Your
simulation time also depends on what the aim of your simulations is and
what you hope to observe. That said, current simulations are generally a
couple of hundred nanoseconds in length. Keep in mind that it's probably
best to perform several simulations - one simulation will only tell you so
much. Repeatability of your observations is important.

You might want to consider using a dodecahedron rather than a cubic box -
the cubic box will require more water molecules to fill completely. As for
the parameters, read the literature. A good starting point is the paper
describing the amber99sb ildn parametrisation. It's also a good idea to
check what parameters have been described in the literature by people
performing similar simulations.

Good luck!
On 23 Feb 2016 8:39 p.m., "Guillem Prats Ejarque" <
Guillem.Prats.Ejarque at uab.cat> wrote:

> 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
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