Periodic Boundary Conditions - Conserved Properties

Conserved Properties

Under periodic boundary conditions, the linear momentum of the system will be conserved, but angular momentum is not conserved because the PBC system is not rotationally symmetric. When applied to the microcanonical ensemble (constant particle number, volume, and energy, abbreviated NVE), using PBC rather than reflecting walls slightly alters the sampling of the simulation due to the conservation of total linear momentum and the position of the center of mass; this ensemble has been termed the "molecular dynamics ensemble" or the NVEPG ensemble. These additional conserved quantities introduce minor artifacts related to the statistical mechanical definition of temperature, the departure of the velocity distributions from a Boltzmann distribution, and violations of equipartition for systems containing particles with heterogeneous masses. The simplest of these effects is that a system of N particles will behave, in the molecular dynamics ensemble, as a system of N-1 particles. These artifacts have quantifiable consequences for small toy systems containing only perfectly hard particles; they have not been studied in depth for standard biomolecular simulations, but given the size of such systems, the effects will be largely negligible.