Hei,
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.
http://www.gromacs.org/ (if you use ubuntu linux you just download the package).
Terveisin Markus
On 2 March 2010 03:37, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--www=http://www.iki.fi/markus.kaukonen
--Markus.Kaukonen.iki.fi
--office: N102 Nano building FIN-02015 TKK
--home: Viinirinne 3 F 12, 02630 Espoo, FIN
--tel: h 045-1242068, w 4518694, 050-5112785
--Rikos ei kannata, eika maatalous
--Suomessa. (Paimio 1998) ---
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 02 2010 - 00:00:02 PST
