Syma Khalid wrote:
Hi Mark,

Firstly, thanks for your prompt response.
If they really are just counter-ions, then simple electrostatics will do that... this is a side-issue, however.

Please can you explain the above?

If you take a point charge and a blob with opposite charge and do some vacuum dynamics, they'll eventually stick together whether you use PBC or not.

Will the ions simply collapse onto my
protein?

Don't know. The point is that they won't be moving like they're in a medium with a substantial dielectric and viscous flow, as I was hinting last email and David Mobley has now said.

The counter ions are simply to there to give me an overall neutral system.
Is there some other way I can get a neutral system?

That depends what physical question you are trying to answer with your protein-without-solvent simulation. You might be better served neutralizing the side chains by changing (e.g.) NH4+ to NH3, or doing implicit solvent simulations without neutralizing, or getting solvent.

Mark
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