AMBER Archive (2009)
Subject: RE: [AMBER] A confusion about tutorial B1
From: Houyang Chen (houyangchen2008_at_hotmail.com)
Date: Tue May 05 2009 - 12:39:18 CDT
Thanks so much!
To David: yes, i write the wrong word. it is "explicit".
Thanks & Best wishes
> From: ross_at_rosswalker.co.uk
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] A confusion about tutorial B1
> Date: Tue, 5 May 2009 08:29:23 -0700
> Hi Houyang,
> > Is there any rules or skill to choose a truncated octahedron when we
> > do minimization and MD in implicit solvent?
> Not any hard and fast rules. Truncated octahedron's can be a little tricky
> since some visualization programs don't deal with them properly.
> Realistically though it comes down to whether your system is likely to
> rotate such that it gets close to the box edges or not. If it likely won't
> then an orthorhombic cell can be more efficient in terms of the number of
> waters required. If you need a cell that is close to cubic to deal with
> rotation or if you have a very spherical solute then truncated octahedron
> can save you some on the numbers of waters you need.
> At the end of the day though it is really just dealers choice.
> All the best
> |\oss Walker
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
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