AMBER Archive (2005)

Subject: Re: AMBER: using periodic boundary conditions to create infinite double helix

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 16 2005 - 18:10:17 CST

On Wed, Nov 16, 2005, Kenley Barrett wrote:

> Also, could somebody please direct me
> to the leap source code in which periodic boundary conditions are set?

Leap doesn't really know much about periodic boundary conditions. It can
"solvate" a system using a rectangular unit cell, or a truncated octahedron.
These two options are hard-wired: I don't think(?) that it has any general
notion of periodicity. Also, it doesn't know how to find minimum images, or
anything else related to the enegies of periodic systems.

I could be wrong...there is hidden stuff inside LEaP known to only a few
people :-)

I recognize that this may not help much....dac

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