AMBER Archive (2009)

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

From: Ross Walker (
Date: Tue May 05 2009 - 10:29:23 CDT

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:- |
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