[gmx-users] periodic boundary conditions

[Mark Abraham]

Hi,

On Wed, Jul 13, 2016 at 5:50 PM Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> 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?
>

Sure, but that's not the point. The point revolves around whether the
properties of your simulation system suitably resemble those found in the
real world. If that's a single cylinder of lipid suspended in some other
milieu, then neither of the periodic systems is particularly representative.


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

Yeah, but only you know whether you are trying to study a
pseudo-crystalline form, or something else? The former is easier, because
you can accept periodicity as part of a model, but the conclusions may not
be applicable outside of that modelling regime...

Mark

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
> > >
> > >
> > >
> > > --
> > > *Rewards work better than punishment ...*
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