| BFGS | Broyden-Fletcher-Goldfarb-Shanno minimisation algorithm [1–3] |
| BFM | Bellman-Ford-Moore algorithm |
| BKL | Bortz-Kalos-Lebowitz algorithm |
| BLJ | Binary Lennard-Jones potential |
| CG | Conjugate Gradient |
| CHARMM | Chemistry at HARvard Molecular Modelling program [4] |
| CHARMM19 | United-atom CHARMM force field [5] |
| CHARMM22 | All-atom CHARMM force field [6] |
| CPU | Central Processing Unit |
| CS | Chain-of-States approach |
| DFP | Davidon-Fletcher-Powell optimisation method |
| DGT | Dense-optimised Graph Transformation method |
| DNEB | Doubly Nudged Elastic Band method [7] |
| DPS | Discrete Path Sampling method [8–10] |
| EEF1 | Effective Energy Function 1 solvation potential [11] |
| EF | Eigenvector-Following method [12–24] |
| GT | Graph Transformation method |
| KMC | Kinetic Monte Carlo method |
| L-BFGS | Limited memory version of the BFGS algorithm [2] |
| LJ | Lennard-Jones potential |
| | |
| LST | Linear Synchronous Transit method |
| MB | Müller-Brown surface [25] |
| MCAMC | Monte Carlo with Absorbing Markov Chains [26] |
| MD | Molecular Dynamics method |
| MM | Matrix Multiplication method |
| NEB | Nudged Elastic Band method [27–30] |
| NMR | Nuclear Magnetic Resonance |
| NR | Newton-Raphson approach [31] |
| ORT | Overall Rotation and Translation |
| PDB | Protein Data Bank |
| PES | Potential Energy Surface |
| QST | Quadratic Synchronous Transit method |
| QVV | Quenched Velocity Verlet minimisation algorithm [27] |
| RMS | Root-Mean-Square |
| SDGT | A version of the GT method that is a combination of SGT and DGT |
| SGT | Sparse-optimised Graph Transformation method |
| SMM | Sparse-optimised Matrix Multiplication method |
| SQVV | Slow-response Quenched Velocity Verlet minimisation algorithm [7] |
| SRW | Simple Random Walk |
| VV | Velocity Verlet integrator [32] |