AMBER Archive (2009)

Subject: Re: [AMBER] Restraining counterions?

From: Bill Ross (
Date: Tue Apr 28 2009 - 13:59:52 CDT

> During the restrained preliminary procedures (density
> equilibration, heating) with a protein in a hydrated lipidic membrane,
> and an extra layer of water, are Na+ counterions (added to neutralize
> the protein charges) to be treated as WAT, i.e. never restrained? Some
> Na+ are inside the hydrated lipidic layer, others in the surrounding
> water layer (positioned by leap'd "addions").

I would definitely not restrain the addions ions, because having
been placed on purely theoretical grounds they would need equilibration.
If there is empirical justification for the placement of the other ions,
I would likely restrain them.


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