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.rosswalker.co.uk
> To: amber.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.ambermd.org [mailto:amber-bounces.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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Received on Wed May 20 2009 - 14:38:45 PDT
