AMBER Archive (2008)

Subject: Re: AMBER: help me for filling a nanotube with water??

From: Markus Kaukonen (markus.kaukonen_at_iki.fi)
Date: Wed Aug 13 2008 - 01:29:48 CDT

Dear Dr Jaber Jahanbin Sardroodi,

I'm not sure at all how well Amber MM force field is suitable for nanotubes.
What I know is that nanotubes have been simulated with the
density-functional based tight-binding method
which is in amber (it is called QM in this context). So maybe you
could try using Amber-QM for nanotubes.

I'm also starting to look at this business, so all comments are welcome.

Probably if you do not have any organic molecules in your system, some
other molecular mechanics program than AMBER might be computationally
much more efficient, with a force field tailored for carbon.

Terveisin, Markus

On Tue, Aug 5, 2008 at 4:39 AM, Jaber Jahanbin Sardroodi
<jsardroodi_at_azaruniv.edu> wrote:
> Dear Amber professional,
>
> I need to fill a carbon nanotube with water molecules (using leap),
> unfortunately I do not know what I do. Can anyone help me?
> Sincerely,
>
> Dr Jaber Jahanbin Sardroodi
> Department of Chemistry, Faculty of Basic Sciences, Azarbaijan
> University of Tarbiat Moallem, Tabriz, Iran
> 

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