[gmx-users] langevin dynamics
Mark.Abraham at anu.edu.au
Wed Oct 31 02:55:52 CET 2007
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
> Will the ions simply collapse onto my
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.
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