  Molecular simulation technologies have afforded researchers a unique look
into the nanoscale interactions driving physical processes. However, a
limitation for molecular dynamics (MD) simulations is that they must be
performed on finite-sized systems in order to map onto computational resources.
To minimize artifacts arising from finite-sized simulation systems, it is
common practice for MD simulations to be performed with periodic boundary
conditions (PBC). However, in order to calculate specific physical properties,
such as mean square displacements to calculate diffusion coefficients,
continuous particle trajectories where the atomic movements are continuous and
do not jump between cell faces are required. In these cases, modifying atomic
coordinates through unwrapping schemes are an essential post-processing tool to
remove these jumps. Here, two established trajectory unwrapping schemes are
applied to 1us wrapped trajectories for a small water box. The existing schemes
can result in spurious diffusion coefficients, long bonds within unwrapped
molecules, and inconsistent atomic coordinates when coordinates are rewrapped
after unwrapping. We determine that prior unwrapping schemes do not account for
changing periodic box dimensions, and introduce an additional correction term
to the existing displacement unwrapping scheme by von Bulow et al. to correct
for these artifacts. We also demonstrate that the resulting algorithm is a
hybrid between the existing heuristic and displacement unwrapping schemes.
After treatment with this new unwrapping scheme, molecular geometries are
correct even after long simulations. In anticipation for longer molecular
dynamics trajectories, we develop implementations for this new scheme in
multiple PBC handling tools.
