AMBER Archive (2005)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Nov 16 2005 - 18:34:53 CST

> > 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 :-)

The setBox cmd is the other place I know of where a box is set.

One way to figure out any program from source code is to grep the commands
it takes in the source, e.g.

% grep -i setbox *.c

and then look for the most promising strings in the relevant files and
work from there with more searches and greps.

Bill
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