AMBER Archive (2005)

Subject: AMBER: How to wrap a truncated octahedron water box into the primary box?

From: Xioling Chuang (xioling_c_at_hotmail.com)
Date: Sat Nov 26 2005 - 04:19:44 CST

Dear All,

I have used a truncated octahedron box of water for MD simulations with
setting iwrap=0. After the simulation, I used "ptraj" with command "image"
to wrap coordinates, as below;

trajin md1.mdcrd
trajout md1.img
center :1-20
image familiar
go

As the result, the simulation box does not look like the truncated
octahedron, unlike the starting coordinates. It seem to be a distorted
octahedron. Any suggestion is welcome.
More questions, does setting "iwrap=1" effact some calculations? If yes,
what kind of such calculations?
Thank you very much in advance.
--------
Xioling

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