AMBER Archive (2008)

Subject: AMBER: double strand DNA break up (imaging)

From: Seth Lilavivat (
Date: Thu Apr 24 2008 - 13:53:44 CDT

Dear Amber users,

During my simulation my DNA approaches the edge of the box and I get one
strand on one side of the box and the other strand on the other side. I am
using NAMD for the simulations and generating .dcd files ( "wrapAll" is
"on"). When I reimage the trajectory using ptraj I still get the
displacement of the two strands. Is there anything I can do about this? My
ptraj script looks like this:

trajin ../output/prod1-5ns.dcd
trajin ../output2/prod5-10ns.dcd
trajout prod1-10ns.dcd
center :1-23
image :1-23 bymask :1-23
strip :WAT


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