Thank you for your valuable information. what are the precautions take in a
long simulation.
On Thu, Feb 17, 2011 at 2:27 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Feb 16, 2011 at 3:08 PM, haris p <hariskalikav.gmail.com> wrote:
> > 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?
>
> I believe the way that Sander wraps molecules based on whether the
> geometric center of the molecule is outside the boundaries of the unit
> cell. So if the geometric center of both DNA strands are at the edge
> of the unit cell but not quite outside the boundaries, it may look
> like the DNA is sticking out into nowhere. Again, this is just a
> visualization artifact; the DNA strands are still interacting with
> solvent on the opposite side of the unit cell.
>
> -Dan
>
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Received on Wed Feb 16 2011 - 13:30:10 PST
