AMBER Archive (2006)

Subject: Re: AMBER: set a trucated octahedron box in Leap

From: David A. Case (
Date: Tue Sep 12 2006 - 10:03:24 CDT

On Tue, Sep 12, 2006, Vlad Cojocaru wrote:
> Of course I did that but the problem is that I need also a top file
> which contains the periodicity info ... Without box info in the top
> file, periodic MD wont run ... So, I will set the IFBOX to 2 and then
> copy the %FLAG BOX DIM from the initial top file ... Is there anything
> else I should consider?

sounds like a some experimenting! (For example, you can check that,
without making the OH-to-H change, you get your original results.)


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to