AMBER Archive (2009)

Subject: Re: [AMBER] Why NaCl or KCl solution?

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed May 27 2009 - 19:50:56 CDT

> In the protein solution, it might be difficult to set PH value for it.

Yes, just to clarify, pH=7 means 1 H+ (or H3O+ as RCW suggested) per 10
million waters. As our simulations are typically much smaller than this,
we typically do not include H+... Perhaps at pH=5 (1 per 100,000 waters)
maybe we'd add it. Certainly at pH=2 or less. What pH are you trying to
represent?

> In stead, people embed protein into NaCl or KCl solution.

Look at experimental conditions... Most involve some salt (it is pretty
hard to pull out all the salt except with severe dialysis; some
biomolecules will denature at low salt); physiological salt is ~200mM.

Also, if the system is net-charged this make no physical sense; the charge
needs to be neutralized. [Technically you can still run with a net-charge
in Ewald (search the archives), but physically it makes no sense].

The choice of salt depends on what experimental conditions you are trying
to reproduce.

--tec3

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