AMBER Archive (2007)

Subject: AMBER: DNA denatures during MD simulation

From: Prashanth Athri (athriprashanth_at_yahoo.com)
Date: Mon Jul 23 2007 - 14:38:12 CDT

Dear AMBER users:
I ran a 50 ns (2500 frames) simulation with a ligand bound to the minor groove of DNA. Right at around 1350'th frame, DNA double strand denatures and immediately, in the next frame, they get back together. This 'phenomenon' repeats itself a couple of times till around the 1600'th frame, and then everything is back to normal.
Any idea how this is happening?

I would appreciate any input. Thanks in advance.
Best,
Prashanth
       
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