AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
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 plan...do some experimenting! (For example, you can check that,
without making the OH-to-H change, you get your original results.)

...dac

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