[gmx-users] periodic boundary conditions

[Mark Abraham]

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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