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.

One major issue that beginners have is when visualizing a trajectory, the molecule(s) does not stay in the centre of the box or it appears that the molecule(s) diffuse out of the box and/or holes are created. This is not a problem or error that is occuring, it is what you should expect.

For a large protein-like molecule under some conditions, it can appear to be sticking out into vacuum, not surrounded by any water or solvent molecules. This is not the case. 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 and the box is not centered around them while performing the simulation.

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 a further explanation, see the GROMACS Manual, Chapter 3 or Periodic boundary conditions.