[gmx-users] langevin dynamics

[Mark Abraham]

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