Re: [AMBER] about ions

From: David A Case <>
Date: Fri, 24 Aug 2012 08:52:28 -0400

On Fri, Aug 24, 2012, Carlos Romero wrote:
> I am simulating proteins and ions, I am using a Generalized Born Method.
> but I need simulate at different concentrations, 0.005, 0.025 0.05 M, and I
> need find a way to calculate how many ions should I add to my simulation

In the GB model, you can directly enter the ionic strength to get screening
at the Debye-Huckel level. Since GB calculations do not use a periodic box,
there is no way to add explicit ions to mimic a certain bulk concentration.

[Another aside/guess: I don't know what kind or size of protein you have
in mind, but I'm guessing you would need extremely precise simulations
to get any reliable dependence on salt concentration at such low ion
concentrations. This may depend on what sorts of analyses you are
planning to do, but you should be aware that the effect of low salt on
proteins is usually pretty subtle.]


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Received on Fri Aug 24 2012 - 06:00:04 PDT
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