Is it possible to add ions to an already solvated system, without adding any more water molecules?

[aniketsh]

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[lohedges]

Potentially you should be able to resolvate a system that was previously solvated and specify a new ion concentration. This would keep all existing water molecules, then adjust the ion concentration accordingly. (This isn't something that I've tested.)

Alternatively, you could replace some of the water molecules in the system with ions. This is not super easy given the current API but I could try to come up with an example script if the above doesn't work. (You could always just edit the top file that is generated if you know what you are doing.)

[aniketsh]

Thanks, @lohedges. My issue, as you describe in option 1, for a membrane system, water molecules are inserted in the membrane. Is there any way to avoid it?

[lohedges]

Ah, I see. We currently don't provide support for membrane simulations. This is a know issue with gmx solvate (our solvation backend) and they describe the issue, and some suggested workarounds here. We don't support the radius option that they suggest, but could look into it if useful. Previously we've found that some of the options don't always behave as you would logically expect, so have limited using them and let people use gmx solvate manually if desired.

[aniketsh]

Thank you for this explaination. I am dealing with a situation wherein the water in the topology file is not continuous, for example: Protein 1 Water 4 Ligand 1 Water 100 In order to put ions in this system with gromacs command, genion, I need to edit gro/pdb and topology file so that the water molecules enties are continuous. With BioSimSpace, I am able to solvate and Ionize these kind of systems , and was wondering do you take care of this ineranlly so that you are able to put ions in this system? and If yes, is it possible to get access to these objects or write them out as gro/pdb and top file?