AMBER Archive (2006)

Subject: Re: AMBER: Periodic boundary condition (PBC)

From: Bill Ross (
Date: Mon Aug 28 2006 - 18:21:57 CDT

> 1) I have loaded my PDB file with force modification file in xleap.
> 2) Then used 'setbox' command to generate the box.

Was the system properly aligned for the box, e.g. if
the system had its vertices rather than faces 'pointing
at' the major planes (x, y, etc), then there would be
a big vacuum to equilibrate.

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