[gmx-users] periodic boundary conditions

[Mohsen Ramezanpour]

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 ...*