[gmx-users] Polymer in periodic boundary conditions again

Ester Chiessi ester.chiessi at uniroma2.it
Fri Nov 15 14:46:52 CET 2002

Thanks Anton for your support.

K.A. Feenstra wrote:

> It might be simply a combination of a non-optimized starting structure with
> your infinite polymer chain. Have you tried to start an 'explicitly connected'
> simulation using the energy-minimized starting conformation that you described?
> You would probably have to re-adjust the x-dimension of your box to get the
> ends of your polymer to line up at the box edges again. You might also need
> or want to re-minimize the system after adjusting the box.
> Are you using pressure coupling? This might also disrupt your periodic
> connectivity.

I'm not using pressure coupling.

I'm going to follow your suggestions.

Before starting however, I have two doubts.

1) When I prepare the polimer inside the box, should the last atom of the chain be
the periodically correspondent of the first? If so, should first and last atom
touch opposite faces of the box, in the right orientation?
Till now, I built my chain as (for example) : A-B-A-B-A-B
and not : A-B-A-B-A-B-A, as I'm describing in this question.

2) During the minimizations, should I have to apply the periodic boundary

Thanks for any helps.


Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462

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