AMBER Archive (2003)

Subject: Re: AMBER: 2D periodic box

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Aug 07 2003 - 12:00:22 CDT

Hi,

You could build a 3D box with an unusually large size in one direction
(say z), that would approximate a 2D situation. I think you want to model
a surface and study some surface properties. THis approximation should be
fine for you.

You also had a question about what force field to use to model
hybrid organic-inorganic interactions (you said something about Al). A
possibility (although limited)
would be to use the MSQ force field developed in the Goddard group at
Caltech (www.wag.caltech.edu)

The MS-Q Force Field for Clay Minerals: Application to Oil Production
    S. Hwang, M. Blanco, E. Demiralp, T. Cagin, and W. A. Goddard III
    J. Phys. Chem. B 105, 4122 (2001)

The MSXX Force Field for the Barium Sulfate-Water Interface
    Yun Hee Jang, Xiao Yan Chang, Mario Blanco, Sungu Hwang, Yongchun
Tang, Patrick Shuler, and William A. Goddard III
    J. Phys. Chem. B, 106, 9951 (2002)

Just a short notice: the MS-Q force field was developed to work in tandem
with the charge equilibration method.

Ioana

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On Thu, 7 Aug 2003, Vikas Varshney wrote:

> Hi all Amber Users,
> I will really appriciate if any of you please let me know how do
> we construct 2 dimensional periodic box.
>
> Thank you very much
>
> Regards,
> Vikas
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