[gmx-users] periodic boundary conditions

[Mohsen Ramezanpour]

Any other comment on this? :-)

On Wed, Jul 13, 2016 at 9:50 AM, 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?
>
> 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
>> >
>> >
>> >
>> > --
>> > *Rewards work better than punishment ...*
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>
>
>
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> *Rewards work better than punishment ...*
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*Rewards work better than punishment ...*