Re: [AMBER] PBC interactions

From: Markus Kaukonen <>
Date: Tue, 2 Mar 2010 09:35:19 +0200

I had the same problem with nanotubes.
Gromacs can handle bonds through the periodic boundary. But it is a
new feature and not too well documented. (if you use ubuntu linux you just download the package).
Terveisin Markus

On 2 March 2010 03:37, Jason Swails <> wrote:
> On Mon, Mar 1, 2010 at 4:51 PM, Ganesh Krishnan <> 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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