GROMACS version: 2023
GROMACS modification: No
Hello everyone, just asking is it possible to make a topology file for a metal ion like Na+?
Sure, here it is, fully self-contained:
[ defaults ]
1 2 yes 0.5 0.8333[ atomtypes ]
Na 11 22.99 0.0000 A 0.243934000000 0.36585[ moleculetype ]
Na 1[ atoms ]
1 Na 1 Na Na 1 1.0 22.9898[ system ]
sodium[ molecules ]
Na 1
But I guess you want to add it to an existing system? Or have Na+ mixed with something else?
Thanks. Yes I want to attach it as a ligand to an existing molecule making it one.
Most likely you don’t want covalent bonds with sodium though, right? Except maybe for some extreme organosodium compounds, it’s going to be a non-covalent sodium-binding site, and then it’s enough to have a sodium ion defined in the topology. Normally ions.itp is automatically embedded in the topology, so you can just add Na 1 to the [ molecules ] section to account for that; the rest will rely on a correct placement of the ion in the structure file.
If you indeed mean a covalent bond, then it gets more complicated.
No its not a covalent bond but rather an ionic one. I just want to couple the ion with the molecule and simulate them together as a whole.
Then, as I said, if the interaction is strong enough, it should be sufficient to have them both in a bound state at the beginning of the simulation, without any additional bonds specified in the topology.
Of course, interactions with ions are never perfectly modeled in additive (non-polarizable) force fields so it’s an open question whether a naive approach will work for you; if it’s somehow experimentally known that the two should stay together and in the simulation they don’t, one can try out different sodium parameter sets, or simply add a restraint. This very much depends on the ultimate purpose of your simulation.
The system am simulating is supposed to contain a partial dissociation between the molecule and the Na counterion. i.e some molecules will be dissociated and others will have the sodium attached the hypothesis is that this will answer some anomalies being recorded for some macroscopic property of the system.
Right, then in theory you’re good to go with a plain non-bonded sodium (that is, no extra additions), just make sure that you’re using a sodium parametrization that was validated with a similar type of interaction - could be papers on crown ethers etc. There are many choices around, but most of them focus on reproducing co-solvent properties rather than binding to ligands.
Ok, thanks. Really appreciate the assistance