\contentsline {section}{\numberline {1}Introduction}{3}
\contentsline {section}{\numberline {2}New in this release}{3}
\contentsline {section}{\numberline {3}Installation}{4}
\contentsline {section}{\numberline {4}Command line arguments and file formats}{4}
\contentsline {subsection}{\numberline {4.1}wham}{5}
\contentsline {subsubsection}{\numberline {4.1.1}Command line arguments for WHAM}{5}
\contentsline {subsubsection}{\numberline {4.1.2}File formats}{6}
\contentsline {subsubsection}{\numberline {4.1.3}Output}{7}
\contentsline {subsection}{\numberline {4.2}wham-2d}{9}
\contentsline {subsubsection}{\numberline {4.2.1}Command line arguments}{9}
\contentsline {subsubsection}{\numberline {4.2.2}File formats}{9}
\contentsline {subsubsection}{\numberline {4.2.3}Output}{10}
\contentsline {section}{\numberline {5}Discussion}{12}
\contentsline {subsection}{\numberline {5.1}Periodicity}{12}
\contentsline {subsection}{\numberline {5.2}Monte Carlo Bootstrap Error Analysis}{12}
\contentsline {subsection}{\numberline {5.3}Using the code for replica exchange simulations}{15}