[gmx-users] periodic boundary conditions

[Mohsen Ramezanpour]

Hi Mark,

Thanks for your reply.

The 6 around 1 setup is also periodic.

I understand this. However, we can argue the same for 6-1 system as well.
Right?

If one edge of this hexagonal deforms, the other side also deforms and in
fact we are applying a symmetry to our system.

The question is: which system is big enough (or suitable) to include this
effect?

What I am interested in is the structural properties of these systems and
lipid-lipid interactions.

Cheers

On Wed, Jul 13, 2016 at 2:23 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> These are different systems. Your 6-around-1 setup (whether itself
> hexagonally periodic or not) has degrees of freedom that the single
> hexagonal cell cannot access. In the latter case, if a wall on one edge of
> the cell deforms, then the corresponding wall on the far side of the cell
> has the matching deformation. However the 6-around-1 can e.g. deform each
> wall of the central hexagonal cell independently. Whether any of these make
> a "correct" model depends what you're trying to model.
>
> Mark
>
> On Wed, Jul 13, 2016 at 2:41 AM Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
> > Dear gromacs-users,
> >
> > Doing simulations on lipid HII phase, I came to a question which I could
> > not get happy with my answer. I appreciate your opinion in advance:
> >
> > Imagine you have a cylinder made of lipids with waters only inside the
> > cylinder, which is long enough and can be run for enough time so that
> there
> > is no problem from sampling aspect. A hexagonal pbc has been also applied
> > to this cylinder properly.
> >
> > In the other system, you have 7 cyinders with 1 central and 6 on the
> > corners of hexagon. The only main difference with the case above will be
> a
> > larger unit cell and less symmetry of the system.
> >
> > Do you expect the results of these two simulations be different, if you
> are
> > interested in structural properties?
> >
> > In other words: does pbc exactly treats the central cylinder as if there
> > was 6 extra cylinders around the it? Can it reproduce the correct
> > environment the central cylinder feels around?
> >
> > Cheer,
> > Mohsen
> >
> >
> >
> > --
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*Rewards work better than punishment ...*