AMBER Archive (2009)

Subject: RE: [AMBER] A confusion about tutorial B1

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 05 2009 - 00:18:43 CDT

Hi Houyang,

For an extended system such as DNA, which could potentially rotate during
the simulation it makes more sense to use a truncated octahedron. One could
potentially use a cubic box but this would require more water than a
truncated octahedron.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Houyang Chen
> Sent: Monday, May 04, 2009 10:02 PM
> To: Amber Maillist
> Subject: [AMBER] A confusion about tutorial B1
>
>
>
> Hi, Amber User,
> I am confused that why set up a truncated octahedral box, not a
> rectangular box, to run
> minimization and MD (in implicit solvent) in tutorial B1
> (http://ambermd.org/tutorials/basic/tutorial1/)?
>
>
> Thanks & Best wishes,
>
> ----------------------------------------------------------------
> Houyang Chen
>
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