AA-MD	All-Atom Molecular Dynamics
ANN	Artificial Neural Networks
BD	Brownian Dynamics
BLUE	Best Linear Unbiased Estimate
CG-MD	Coarse-Grained Molecular Dynamics
CPU	Central Processing Unit
DEM	Discrete Element Method
DOF	Degree of Freedom
DPD	Dissipative Particle Dynamics
FF	Force Field
GPR	Gaussian Process Regression
GPU	Graphics Processing Unit
HBcAg	Hepatitis B Core Antigen
HBcAg${}_2$	HBcAg Dimer
HBV	Hepatitis B Virus
LD	Langevin Dynamics
MDEM	Molecular Discrete Element Method
MD	Molecular Dynamics
NPT	Isothermal-Isobaric Ensemble
PBC	Periodic Boundary Conditions
PDB	Protein Data Bank
PME	Particle Mesh Ewald
PW	Polarizable Water
QM/MM	Quantum Mechanics/Molecular Mechanics
RMS	Root-Mean-Square
RMSD	Root-Mean-Square Distance
SAS	Self-Assembled Structure
SI	Supplementary Information
SPX	Simulation Procedure X
SVD	Singular Value Decomposition
UK	Universal Kriging
VLP	Virus-Like Particles