AMBER	Assisted model building with energy refinement
CHARMM	Chemistry at Harvard Macromolecular Mechanics
DMPC	1,2-Dimyristoyl-sn-glycero-3-phosphocholine
DPPC	Dipalmitoylphosphatidylcholine
GA	Genetic algorithm
Gly	Glycine
Gly-Hyp	Glycyl-hydroxyproline
Gly-Pro-Hyp	Glycylprolylhydroxyproline
GPU	Graphics processing unit
GUI	Graphical user interface
Hyp	Hydroxyproline
K	Lysine
kcal/mol	Kilocalorie per mole
LGA	Lamarckian genetic algorithm
MD	Molecular dynamics
MSD	Mean square displacement
PDB	Protein data bank
PEPT	Peptide transporter
PHT	Peptide histidine transporter
PMEMD	Particle mesh Ewald molecular dynamics
POPC	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Pro	Proline
Pro-Hyp	Prolyl-hydroxyproline
Ps	Picoseconds
Q	Glutamine
RMSD	Root mean square deviation
TIP3P	Transferable intermolecular potential with 3 points
UCSF	The University of California, San Francisco
VMD	Visual molecular dynamics
Å	Angstrom