| CHARMM | Chemistry at HARvard Macromolecular Mechanics |
| EPM2 | Elementary Physical Model 2 |
| MD | Molecular Dynamics |
| MSD | Mean-Squared Displacement |
| MSM-ZD | Murthy, Singer, and McDonald—Zhang and Duan |
| NIST | National Institute of Standards and Technology |
| NMR | Nuclear Magnetic Resonance |
| OPC | Optimal Point Charge |
| OPLS-aa | Optimized Potentials for Liquid Simulations-all atom |
| RMS | Root Mean Square |
| SPC/E | Extended Simple Point Charge |
| TIP4P/2005 | Transferable Intermolecular Potential with 4 Points/2005 |
| TIP5P | Transferable Intermolecular Potential with 5 Points |
| TraPPE | Transferable Potentials for Phase Equilibria |