AMBER Archive (2005)

Subject: AMBER: vdw or center box dimensions, periodicity, and the jagged edge

From: Stern, Julie (jvstern_at_bnl.gov)
Date: Tue Apr 12 2005 - 12:30:38 CDT

Hello,
    How are the vdw and center box dimensions computed using setBox? I
have a grid of hydrocarbon chains which produce a see-saw jagged edge
because
they are placed within a crystal structure, i.e. row 2 is shifted left
compared to rows 1 and 3, etc. So, if the box dimension takes the farthest
atom it finds on all sides as the dimension, does row 2 effectively
experience
the proper wraparound because its edge atom was interior on the right side
and a
farthest atom on the left side?
    Does the vdw option create extra space before wrapping around and does
the center
of the atoms not do justice to interior atoms in a jagged edge? If I set
the box dimension myself, would I set the edges to the interior atoms on an
edge as opposed to the ones
that protrude out?
    I'm currently operating with the vdw option and am seeing edge effects
in
my results.

Thanks.

--Julie
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu