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BFGS Broyden-Fletcher-Goldfarb-Shanno minimisation algorithm [1,2,3]
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 [9,10,8]
EEF1 Effective Energy Function 1 solvation potential [11]
EF Eigenvector-Following method [17,18,12,14,24,13,19,16,22,21,23,20,15]
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 [29,28,27,30]
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]

next up previous contents
Next: GLOSSARY OF SYMBOLS Up: thesis Previous: Contents   Contents
Semen A Trygubenko 2006-04-10