Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib

From: Pengfei Li <>
Date: Wed, 20 Dec 2017 16:57:29 -0600

Hi Yuan,

For the 12-6 model, there are different parameter sets to reproduce different experimental properties (HFE, IOD, and CM parameter sets). And these parameters are water model dependent (i.e. parameters are different for different water models).

For the 12-6-4 model, there is only one parameter set (the 12-6-4 parameter set). And these parameters are also water dependent.

> On Dec 18, 2017, at 12:49 AM, wrote:
> Hi Pengfei,
> I read your article about 12-6-4 LJ-type nonbonded model in explict water.
> It says Rmin, ε for the VDW interactions and the C4 term for the ion-induced dipole interactions.
> For trivalent and tetravalent metal ions, 12-6-4 type parameters for different water model can reproduce the exp. data simualtaneously.
> The parameters you provided are Rmin and ε.
> If they are 12-6 type, are they HFE or IOD parameter set? How about the type of water model?
> Sorry for bothering you.

Do you mean the parameters of As3+ I sent to you? It is a 12-6 IOD parameter set for As3+ with the TIP3P water model (if my memory was right). For the IOD parameter set, their transferability is usually good and could offer similar IOD values when using with different water models.

Kind regards,
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Received on Wed Dec 20 2017 - 15:00:02 PST
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