# [gmx-users] infinite alpha-helix

Nuno R. L. Ferreira nunolf at ci.uc.pt
Thu Dec 2 11:13:15 CET 2004

```David <spoel at xray.bmc.uu.se> escreveu:

> On Wed, 2004-12-01 at 16:03 +0100, herbst at fhi-berlin.mpg.de wrote:
> > Hello all!
> >
> > Is it possible to create the illusion of an infinite alpha-helix by
> > choosing the box size so, that the outer atoms of the helix (which are
> > restrained, of course) touch the box sides and PBC makes it appear
> > infinite? Can the box be choosen in that way or has there to be a distance
> > between atoms and the box side?
> Yes you can do it, but it is tricky how to get the topology. If you have
> a topology you can simulate it with
> pbc=full
>

This is a very nice question ;-)!

Just thinking ... not sure if its correct.
If a helix has a period of x, than I suppose that the periodic box should have
multiples of x. And this is true, only if the helix is very linear. Is this
correct?

How to handle with the common ensembles with this kind of system?
Working under NPT the volume will have slighty changes during the simulation.
In this case, the lenght of the helix should follow the same box lenght
changes. Restraining the outer atoms of the helix, has Anna suggested, does
not allow the helix to change its length, does it?

Working under NVT, that problem of box lenght changes is not a question, and
restraining the outer atoms is possible.

But what about if I would like to allow helix lenght changes, to see any
periodic fluctuations that could exist? Like in bilayers.

And if the helix its not linear, but rather bended, can we simulate an
infinite system?

What's the difference between pbc=full and =xyz? The first one is used for an
infinite molecule system like a helix, and the second one?

If it's tricky to get the topology for that kind of system, what are the
relevant precautions that we must take into consideration?

rgds
N.

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Nuno Ricardo Santos Loureiro da Silva Ferreira
Ph.D student
Grupo de Química Biológica
Departamento de Química
3004-535 Coimbra
Portugal
www.biolchem.qui.uc.pt
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