AMBER Archive (2009)

Subject: Re: [AMBER] Parallelepiped periodic box

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Jan 16 2009 - 13:50:32 CST

On Mon, Jan 12, 2009, Ian Streeter wrote:
>
> In the inpcrd file and rst files, the coordinates of the atoms are given
> using an orthogonal coordinate system, and then the periodic box lengths
> and angles are given at the end of the file. What is the relationship
> between these lengths/angles and the vectors that define the periodic
> box in the orthogonal coordinate system?

See the map_coords() routine in $AMBERHOME/src/nonbond_list.f. These
shows how fractional coordinates in the unit cell are related to
orthogonal ones.

>
> In the prmtop file, the periodic box is defined under the BOX_DIMENSIONS
> flag. But it seems to be defined differently compared to the inpcrd
> file - only one angle is specified, which the amber website says is "the
> angle between the XY and YZ planes in degrees". No other angles may be
> specified. Does this mean the box must be a 90 degree rectangle in the
> XY plane?

The BOX_DIMENSIONS stuff in the prmtop is only present to help with
backward compatibility...the box information is always taken from the
inpcrd or restart file. [It's awkward to change the prmtop file, since
some non-sander programs (perhaps written by other people) may use this
information for simple rectangular or truncated octahedral unit cells.
But fundamentally, amber *really* uses the data in the coordinate file,
not the data in the prmtop file.

...hope this helps...dac

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