The main precautions to take are:
1) Use iwrap=1 so that coordinates don't overflow the restart format limit.
2) Recognize that this can cause visualization artifacts resulting from the
imaging.
3) Center and image your trajectory to get things fitted the way you want
them.
Note that you lose diffusion effects doing this.
Hope this helps,
Jason
On Wed, Feb 16, 2011 at 4:13 PM, haris p <hariskalikav.gmail.com> wrote:
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 16 2011 - 16:30:04 PST
