AMBER Archive (2006)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Sep 12 2006 - 03:48:56 CDT

I think u dont need to have the box info in the prmtop file (if I am
wrong, someone correct me). The box info are read from the inpcrd files.

Best,

On Tue, 12 Sep 2006, Vlad Cojocaru wrote:

> Thanks David for the answer,
>
> 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?
>
> Best wishes
> vlad
>
>
>
> David A. Case wrote:
>
> >On Mon, Sep 11, 2006, Vlad Cojocaru wrote:
> >
> >
> >>I have an equilibrated periodic system (truncated octahedron box) and I
> >>want to do a very small modification of the system using Leap. In the
> >>meantime I want to retain all info regarding periodicity (box shape and
> >>dimensions).
> >>
> >>
> >
> >For truncated octahedron, you probably will have to manually edit the last
> >line of the coordinate file to match what was there in the earlier file
> >(before the change).
> >
> >...good luck...dac
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>
> 

-- 
  Ilyas Yildirim
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