AMBER Archive (2009)

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

From: Houyang Chen (houyangchen2008_at_hotmail.com)
Date: Tue May 05 2009 - 00:24:39 CDT

Hi,ross,

Thanks so much!

Is there any rules or skill to choose a truncated octahedron when we

do minimization and MD in implicit solvent?

Thanks

 

Houyang
 

> From: ross_at_rosswalker.co.uk
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] A confusion about tutorial B1
> Date: Mon, 4 May 2009 22:18:43 -0700
>
> 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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