Re: AMBER: DNA denatures during MD simulation

From: Thomas Cheatham <>
Date: Mon, 23 Jul 2007 13:49:49 -0600 (Mountain Daylight Time)

> 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.

This is likely an imaging issue; if, in fact the DNA did denature and
the strands separated, I would expect that it would be very difficult to
overcome entropy and see the two strands immediately come back together
with a helical geometry.

More than likely, what is happening is that the double strand migrates to
the edge of the box; the center of mass of one strand goes outside and
gets imaged back in (leading to a situation where it looks like the
molecules are separated, but in a periodic sense everything is peachy).
If comes back as teh second molecules center of mass moves out and it is
imaged to its pair.

Assuming you have a 10-mer DNA duplex, for the sake of argument, try

center :1-10 mass origin
image origin center familiar
center :1-20 mass origin
image origin center familiar

in a ptraj script...

-- tec3

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Received on Wed Jul 25 2007 - 06:07:22 PDT
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