On Mon, Mar 1, 2010 at 4:51 PM, Ganesh Krishnan <hereisganesh.yahoo.com> wrote:
> I am trying to simulate an "infinite polymer" system using AMBER. While I understand that bonds cannot go through the periodic boundary, can one end of a molecule interact (non-bonded) with the other end through the periodic boundary? Is there any problem with such an approach?
This is, in fact, what they do. If the box is periodic, one side of
the box necessarily interacts with the other side (since it is, in
fact, directly adjacent in the next box). Also, because bonds cannot
cross periodic boundaries, you can only have (and will always have)
non-bonded interactions felt through adjacent boxes. (Note that while
these boxes aren't printed out to coordinate files and can't be
visualized easily, adjacent boxes are present in the simulation).
However, that being said, an infinite polymer probably requires bonds,
not just non-bonded interactions. Perhaps others can comment more on
this point.
Hope this helps,
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Mar 01 2010 - 18:00:02 PST
