Re: [AMBER] Fwd: About long simulation

From: Daniel Roe <>
Date: Wed, 16 Feb 2011 14:34:35 -0500


On Wed, Feb 16, 2011 at 10:47 AM, haris p <> wrote:
> first production run itself. But after two steps ( 200ps each) our DNA split
> apart in to two strands. Still the work continues and in the next step the
> strand recombine and proceeds. Na+ ions were also moved apart. We were

What you are describing is expected behavior from iwrap=1. The way
that Leap builds DNA is to consider each strand as a separate
molecule. Since molecule wrapping with iwrap=1 is done on a
per-molecule basis, this means occasionally one strand of DNA may get
wrapped while the other one does not. The strands may look "split",
but since the unit cell is periodic this is a visual artifact only and
will have no effect on the energy. You can use ptraj to image your DNA
back into the center of the box. So say for example you have DNA with
residues 1-12 comprising strand 1 and 13-24 comprising strand 2, your
ptraj input would look like:

trajin DNA.crd
center :1-12
image origin center
center :1-24
image origin center
trajout DNA.imaged.crd

If your box is a truncated octahedron add the 'familiar' keyword to
the image commands. Hope this helps.


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Received on Wed Feb 16 2011 - 12:00:06 PST
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