AMBER Archive (2005)

Subject: AMBER: periodic boundaries and repeating structure

From: Stern, Julie (jvstern_at_bnl.gov)
Date: Thu Apr 14 2005 - 12:55:09 CDT

Hello,
    My structure is different from a protein in solvent situation where a
water
leaves one side of a periodic box and comes in the box on the other side. I
have a grid of chains that have to be effectively replicated through
periodicity, i.e.
the left most chain inside the box should effectively be the next chain over
from the right most chain inside the box.

With setBox center or vdw, my structure won't be replicated properly. Those
options would add spaces and create edge effects.

What else can I do?

Thanks for any suggestions.

--julie
    
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