%!TEX root = thesis.tex

\makeglossaries
\newacronym{MD}{MD}{molecular dynamics}
\newacronym{LJ}{LJ}{Lennard-Jones}
\newacronym{PME}{PME}{particle-mesh Ewald}
\newacronym{HCN}{HCN}{hyperpolarization-activated cyclic nucleotide-gated}
\newacronym{VSD}{VSD}{voltage sensor domain}
\newacronym{LBD}{LBD}{ligand-binding domain}
\newacronym{PD}{PD}{pore domain}
\newacronym{SF}{SF}{selectivity filter}
\newacronym{TPCs}{TPCs}{two-pore channels}
\newacronym{KTN}{KTN}{nucleotide-binding domain}
\newacronym{Na}{Na\textsuperscript{+}}{sodium}
\newacronym{K}{K\textsuperscript{+}}{potassium}
\newacronym{Cl}{Cl\textsuperscript{-}}{chloride}
\newacronym{Ca}{Ca\textsuperscript{2+}}{calcium}
\newacronym[firstplural=voltage-gated ion channels (VGICs)]{VGIC}{VGIC}{voltage-gated ion channel}
\newacronym{If}{I\textsubscript{f}}{funny current}
\newacronym[firstplural=transmembrane helices (TMHs)]{TMH}{TMH}{transmembrane helix}
\newacronym{Kv}{K\textsubscript{V}}{voltage-gated potassium channel}
\newacronym{Kchannel}{K\textsuperscript{+}~channel}{potassium channel}
\newacronym{SAN}{SAN}{sinoatrial node}
\newacronym{CNBD}{CNBD}{cyclic-nucleotide binding-domain}
\newacronym{cAMP}{cAMP}{cyclic-adenosine monophosphate}
\newacronym{cGMP}{cGMP}{cyclic-guanosine monophosphate}
\newacronym{TRIP8b}{TRIP8b}{tetratricopeptide repeat-containing Rab8b-interacting protein}
\newacronym{HCND}{HCND}{HCN domain}
\newacronym{AA}{AA}{amino acid}
\newacronym{PBC}{PBC}{periodic boundary conditions}
\newacronym{PMF}{PMF}{potential of mean force}
\newacronym{CV}{CV}{collective variable}
\newacronym{MFEP}{MFEP}{minimal free energy pathway}
\newacronym{FES}{FES}{free energy surface}
\newacronym{US}{US}{umbrella sampling}
\newacronym{WHAM}{WHAM}{Weighted Histogram Analysis Method}
\newacronym{TEA}{TEA\textsuperscript{+}}{tetraethylazanium}
\newacronym{POPC}{POPC}{palmitoyloleoylphosphatidylcholine}
\newacronym{VdW}{VdW}{Van der Waals}
\newacronym{RDF}{RDF}{radial distribution function}
\newacronym{COM}{COM}{center-of-mass}
\newacronym{CF}{CF}{cystic fibrosis}
\newacronym{CFTR}{CFTR}{cystic fibrosis transmembrane conductance regulator}
\newacronym{NEB}{NEB}{nudged elastic band}
\newacronym{TST}{TST}{transition state theory}
\newacronym{wt}{wt}{wildtype}

\newcommand{\K}{\gls{K}\xspace}
\newcommand{\Na}{\gls{Na}\xspace}
\newcommand{\Cl}{\gls{Cl}\xspace}
\newcommand{\Ca}{\gls{Ca}\xspace}
\newcommand{\Calpha}{C\subs{$\alpha$}\xspace}
\newcommand{\s}[1]{s\textsubscript{#1}\xspace}
\newcommand{\p}[1]{p\textsubscript{#1}\xspace}
\newcommand{\z}[1]{z\textsubscript{#1}\xspace}
\newcommand{\Kchannel}{\K~channel\xspace}
\newcommand{\Kchannels}{\K~channels\xspace}
\newcommand{\KK}{\gls{K}/\gls{K}\xspace}
\newcommand{\NaNa}{\gls{Na}/\gls{Na}\xspace}
\newcommand{\KNa}{\gls{K}/\gls{Na}\xspace}
\newcommand{\NaK}{\gls{Na}/\gls{K}\xspace}
\newcommand{\KKK}{\gls{K}/\gls{K}/\gls{K}\xspace}
\newcommand{\NaNaNa}{\gls{Na}/\gls{Na}/\gls{Na}\xspace}
\newcommand{\KNaNa}{\gls{K}/\gls{Na}/\gls{Na}\xspace}
\newcommand{\NaKK}{\gls{Na}/\gls{K}/\gls{K}\xspace}

\glsaddall