AMBER Archive (2001)

Subject: terminal base pair opening 2

From: Peter Varnai (Peter.Varnai_at_ibpc.fr)
Date: Mon Apr 02 2001 - 08:46:06 CDT

I should have added that my simulation is in explicit
water and one of the terminal base-pairs (AT) opened after
600 ps and stayes there for the next 800 ps at least. 

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Dear Amber users,

I wonder what people think of the terminal base
pair opening of short (e.g. 12mer) DNA sequences
in MD simulations at 300 K. Should it be prevented
by e.g. small distance constraints between H-bonded
atoms to mimic a normal stacking in a longer DNA 
strech, or it would introduce a bigger artifact in
the model. Would this effect be significant 3-4 steps
away? 

Thanks for your comments.

Peter Varnai