hi,everyone,
Thanks so much!
To David: yes, i write the wrong word. it is "explicit".
Thanks & Best wishes
Houyang
> From: ross.rosswalker.co.uk
> To: amber.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
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_________________________________________________________________
More than messages–check out the rest of the Windows Live™.
http://www.microsoft.com/windows/windowslive/_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 14:45:26 PDT
