Thanks for the quick reply. Why part of the DNA comes outside the truncated
octahedron box when put iwrap = 1 without spliting in to two strands?
On Thu, Feb 17, 2011 at 1:04 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Feb 16, 2011 at 10:47 AM, haris p <hariskalikav.gmail.com> 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.
>
> -Dan
>
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Received on Wed Feb 16 2011 - 12:30:04 PST
