Re: AMBER: DNA denatures during MD simulation

From: Carlos Simmerling <>
Date: Mon, 23 Jul 2007 15:44:35 -0400

is it from imaging across the periodic box? try using the image
command in ptraj.
there have been lots of examples posted in the archives.

On 7/23/07, Prashanth Athri <> wrote:
> 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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Received on Wed Jul 25 2007 - 06:07:22 PDT
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