Hi Li,
You can consult the section 3.6 in the AMBER 16 manual: http://ambermd.org/doc12/Amber16.pdf <http://ambermd.org/doc12/Amber16.pdf> for the ion parameters.
I don’t have any experience about using all atom ion parameters into the MARTINI CG model. Usually the ion parameters are water model dependent and in the AMBER force field the atomic ion parameters are designed for TIP3P, SPC/E, and TIP4PEW water models separately. Hope it helps.
Kind regards,
Pengfei
> On Aug 17, 2016, at 2:18 PM, li he <parachuternewyork.gmail.com> wrote:
>
> Dear ambers,
> I am not sure if I'd better post my question here, but the martini forum
> http://www.cgmartini.nl/index.php/forum does not allow me register and
> post my
> question there.
> I am trying to simulate some KCl solution, but only find martini CG Na+
> parameters
> at http://cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp
> I am wondering where I can find martini parameters for K+ ion, or can I
> just use martini
> Na+ parameters for K+?
> If there is a martini parameter of K+, I could image it should be Qd bead
> with +1 charge, exactly the same as Na+ parameters at the above link. Yes,
> it is upsetting to use the same parameter for Na+ and K+, but we have to
> admit the current martini force field is not very fine tuned, thus have to
> just use Na+ martini parameters at the above link for K+ if we want to
> simulate CG KCl or martini KCl anyway? Can this way be justified if the
> simulation results agree with the results of other studies, either
> experiments or simulations?
> Thanks a lot for your kind help, and any suggestion or comment is very
> welcome.
> Yours
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Received on Wed Aug 17 2016 - 14:00:02 PDT
