Periodic Boundary Conditions

Periodic boundary conditions (PBC) are used in molecular dynamics simulations to avoid problems with boundary effects caused by finite size, and make the system more like an infinite one, at the cost of possible periodicity effects.

Beginners visualizing a trajectory sometimes think they are observing a problem when

• the molecule(s) does not stay in the centre of the box, or
• it appears that (parts of) the molecule(s) diffuse out of the box, or
• holes are created, or
• broken molecules appear, or
• crazy bonds all across the simulation cell appear.

This is not a problem or error that is occuring, it is what you should expect.

The existence of PBC means that any atom that leaves a simulation box by, say, the right-hand face, then enters the simulation box by the left-hand face. In the example of a large protein, if you look at the face of the simulation box that is opposite to the one from which the protein is protruding, then a hole in the solvent will be visible. The reason that the molecule(s) move from where they were initially located within the box is (for the vast majority of simulations) they are free to diffuse around. And so they do. They are not held in a magic location of the box. The box is not centered around anything while performing the simulation. Molecules are not made whole as a matter of course.

These visual issues can be fixed after the conclusion of the simulation by judicious use of the optional inputs to trjconv to process the trajectory files. Similarly, analyses such as RMSD of atomic positions can be flawed when a reference structure is compared with a structure that needs adjusting for periodicity effects, and the solution with trjconv follows the same lines. Some complex cases needing more than one operation will require more than one invocation of trjconv in order to work.

For further information, see the GROMACS Manual, Chapter 3.