Re: [AMBER] effect neutralizing ions on value of "saltcon" in generalized Born model

From: Brian Radak <>
Date: Mon, 1 Oct 2012 16:58:22 -0400

The prevailing wisdom, at least in AMBER, is that you should almost never
include explicit ions in implicit solvent simulations (maybe if they are
strongly associated, etc. but that is a special case). You will probably
not get physical results if you do include them.

Also, depending on the force field you are using, I think igb=8 is
generally a superior model and the new standard.


On Mon, Oct 1, 2012 at 4:36 PM, Sajeewa Pemasinghe <>wrote:

> Hi all,
> I am running MD on a protein having about 3400 atoms. I am going to use
> implicit solvation (igb=7). The protein has an unperturbed charge of (-10).
> If I add 10 Na+ ions to neutralize will I have to consider that when
> specifying the value of saltcon in generalized Bone model? This might
> sound silly but the manual says that saltcon specifies the concentration(M)
> of 1-1 mobile counterions in solution. So if I add 10 Na+ ions how should I
> determine the value for saltcon?
> Thank you
> Sajeewa Dewage
> _______________________________________________
> AMBER mailing list

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Received on Mon Oct 01 2012 - 14:00:02 PDT
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