= Centering Molecules =

Centering molecules means to place in a specific way into a domain that adheres to a specific set of boundary conditions. Here, these boundary conditions are either open or periodic. Centering thus works both ways: It may change just the molecular coordinates via translation but also it may change the box size itself.

== Changing the box ==

=== ... adding empty boundary ===

This case is used when we want to have open boundary conditions but simulate this in an periodic boundary setting. In most cases this is approximated by placing the periodic images of the molecules sufficiently far away from each other. Or, in other words, to put enough empty space in between. For this we may use
{{{
./molecuilder -i <input> --add-empty-boundary-condition "5,5,5"
}}}
which translates the atoms in ''<input>'' in such a manner that they will leave a 5 Angstroem wide void space till each face of a rectangular domain.

=== ... center in (new) box ===

=== ... center on edge ===

This is used when the code works on open boundary conditions and the coordinates should be shifted to sensible values initially.
{{{
./molecuilder -i <input> --center-edge
}}}
This will place the atom in the corner closest to origin on the origin such that the remainer of the atoms occupy only the positive octant of the three-dimensional space, setting the bounding box as small such that all atoms are just contained within.

=== ... change box ===


== Changing the molecules ==

=== ... bound in box ===