\contentsline {section}{\numberline {1}Introduction}{2}{section.1}
\contentsline {section}{\numberline {2}New in this release}{2}{section.2}
\contentsline {section}{\numberline {3}Installation}{3}{section.3}
\contentsline {section}{\numberline {4}Command line arguments and file formats}{4}{section.4}
\contentsline {subsection}{\numberline {4.1}wham}{4}{subsection.4.1}
\contentsline {subsubsection}{\numberline {4.1.1}Command line arguments for WHAM}{4}{subsubsection.4.1.1}
\contentsline {subsubsection}{\numberline {4.1.2}File formats}{5}{subsubsection.4.1.2}
\contentsline {subsubsection}{\numberline {4.1.3}Output}{6}{subsubsection.4.1.3}
\contentsline {subsection}{\numberline {4.2}wham-2d}{8}{subsection.4.2}
\contentsline {subsubsection}{\numberline {4.2.1}Command line arguments}{8}{subsubsection.4.2.1}
\contentsline {subsubsection}{\numberline {4.2.2}File formats}{9}{subsubsection.4.2.2}
\contentsline {subsubsection}{\numberline {4.2.3}Output}{10}{subsubsection.4.2.3}
\contentsline {section}{\numberline {5}Discussion}{11}{section.5}
\contentsline {subsection}{\numberline {5.1}Periodicity}{11}{subsection.5.1}
\contentsline {subsection}{\numberline {5.2}Monte Carlo Bootstrap Error Analysis}{11}{subsection.5.2}
\contentsline {subsection}{\numberline {5.3}Using the code for replica exchange simulations}{14}{subsection.5.3}