AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue May 05 2009 - 10:41:54 CDT

On Tue, May 05, 2009, Ross Walker wrote:
>
> > Is there any rules or skill to choose a truncated octahedron when we
> > do minimization and MD in implicit solvent?

Just a note: this question doesn't make good sense to me. Amber's
implicit solvent routines do not impose periodic boundaries at all, and don't
have a box shape. If fact, you are not allowed to set igb>0 and ntb>0 at the
same time.

If you meant "explicit solvent" rather than "implict solvent", then Ross'
answer provides good advice.

...dac

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