Just to close the loop -- Dr. Cheatham was right, it was just an imaging issue and the ptraj cmds below worked!
Thanks.
Thomas Cheatham <tec3.utah.edu> wrote:
> 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 - 06:07:25 PDT
