\BOOKMARK [0][-]{chapter*.1}{Table of Contents}{}
\BOOKMARK [0][-]{chapter*.2}{List of Figures}{}
\BOOKMARK [0][-]{chapter*.3}{List of Tables}{}
\BOOKMARK [0][-]{section*.4}{List of Acronyms}{}
\BOOKMARK [0][-]{chapter.1}{Introduction}{}
\BOOKMARK [1][-]{section.1.1}{New features in version 3.0}{chapter.1}
\BOOKMARK [1][-]{section.1.2}{User feedback}{chapter.1}
\BOOKMARK [0][-]{chapter.2}{Installing nMOLDYN}{}
\BOOKMARK [1][-]{section.2.1}{Unix users}{chapter.2}
\BOOKMARK [1][-]{section.2.2}{Windows users}{chapter.2}
\BOOKMARK [0][-]{chapter.3}{Input and output files}{}
\BOOKMARK [1][-]{section.3.1}{NetCDF file format}{chapter.3}
\BOOKMARK [1][-]{section.3.2}{PDB file format}{chapter.3}
\BOOKMARK [1][-]{section.3.3}{nMOLDYN preference file}{chapter.3}
\BOOKMARK [1][-]{section.3.4}{nMOLDYN selection files}{chapter.3}
\BOOKMARK [1][-]{section.3.5}{nMOLDYN autostart files}{chapter.3}
\BOOKMARK [1][-]{section.3.6}{nMOLDYN input files}{chapter.3}
\BOOKMARK [0][-]{chapter.4}{Using nMOLDYNfrom the Graphical User Interface}{}
\BOOKMARK [1][-]{section.4.1}{The File menu}{chapter.4}
\BOOKMARK [2][-]{subsection.4.1.1}{Load NetCDF file}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.2}{Trajectory conversion}{section.4.1}
\BOOKMARK [3][-]{subsubsection.4.1.2.1}{Amber to MMTK}{subsection.4.1.2}
\BOOKMARK [3][-]{subsubsection.4.1.2.2}{CHARMM/X-PLOR to MMTK}{subsection.4.1.2}
\BOOKMARK [3][-]{subsubsection.4.1.2.3}{DL\137POLY to MMTK}{subsection.4.1.2}
\BOOKMARK [3][-]{subsubsection.4.1.2.4}{Discover to MMTK}{subsection.4.1.2}
\BOOKMARK [3][-]{subsubsection.4.1.2.5}{Forcite to MMTK}{subsection.4.1.2}
\BOOKMARK [3][-]{subsubsection.4.1.2.6}{NAMD to MMTK}{subsection.4.1.2}
\BOOKMARK [3][-]{subsubsection.4.1.2.7}{VASP to MMTK}{subsection.4.1.2}
\BOOKMARK [2][-]{subsection.4.1.3}{Frame snapshot}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.4}{Convert NetCDF to ASCII}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.5}{Convert ASCII to NetCDF}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.6}{Preferences}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.7}{Quit}{section.4.1}
\BOOKMARK [1][-]{section.4.2}{The Analysis menu}{chapter.4}
\BOOKMARK [2][-]{subsection.4.2.1}{Weighting scheme}{section.4.2}
\BOOKMARK [2][-]{subsection.4.2.2}{Atom selection}{section.4.2}
\BOOKMARK [3][-]{subsubsection.4.2.2.1}{Subset selection}{subsection.4.2.2}
\BOOKMARK [3][-]{subsubsection.4.2.2.2}{Deuteration selection}{subsection.4.2.2}
\BOOKMARK [3][-]{subsubsection.4.2.2.3}{Group selection}{subsection.4.2.2}
\BOOKMARK [2][-]{subsection.4.2.3}{Running modes}{section.4.2}
\BOOKMARK [2][-]{subsection.4.2.4}{The Dynamics menu}{section.4.2}
\BOOKMARK [3][-]{subsubsection.4.2.4.1}{Mean-Square Displacement}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.2}{Root Mean-Square Deviation}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.3}{Radius of gyration}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.4}{Angular Correlation}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.5}{Velocity Autocorrelation Function}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.6}{Density Of States}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.7}{Pass-Band Filtered Trajectory}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.8}{Global Motion Filtered Trajectory}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.9}{Rigid-Body Trajectory}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.10}{Center Of Mass Trajectory}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.11}{Auto-Regressive Analysis}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.12}{Quasi Harmonic Analysis}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.13}{Reorientational Correlation Function}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.14}{Angular Velocity AutoCorrelation Function}{subsection.4.2.4}
\BOOKMARK [3][-]{subsubsection.4.2.4.15}{Angular Density Of States}{subsection.4.2.4}
\BOOKMARK [2][-]{subsection.4.2.5}{The Scattering menu}{section.4.2}
\BOOKMARK [3][-]{subsubsection.4.2.5.1}{Introduction}{subsection.4.2.5}
\BOOKMARK [3][-]{subsubsection.4.2.5.2}{Dynamic Coherent Structure Factor}{subsection.4.2.5}
\BOOKMARK [3][-]{subsubsection.4.2.5.3}{Dynamic Coherent Structure Factor \(AR Model\)}{subsection.4.2.5}
\BOOKMARK [3][-]{subsubsection.4.2.5.4}{Dynamic Incoherent Structure Factor}{subsection.4.2.5}
\BOOKMARK [3][-]{subsubsection.4.2.5.5}{Dynamic Incoherent Structure Factor \(AR Model\)}{subsection.4.2.5}
\BOOKMARK [3][-]{subsubsection.4.2.5.6}{Dynamic Incoherent Structure Factor \(Gaussian Approximation\)}{subsection.4.2.5}
\BOOKMARK [3][-]{subsubsection.4.2.5.7}{Elastic Incoherent Structure Factor}{subsection.4.2.5}
\BOOKMARK [3][-]{subsubsection.4.2.5.8}{Static Coherent Structure Factor}{subsection.4.2.5}
\BOOKMARK [3][-]{subsubsection.4.2.5.9}{Smoothed Static Coherent Structure Factor}{subsection.4.2.5}
\BOOKMARK [2][-]{subsection.4.2.6}{The Structure menu}{section.4.2}
\BOOKMARK [3][-]{subsubsection.4.2.6.1}{Pair Distribution Function}{subsection.4.2.6}
\BOOKMARK [3][-]{subsubsection.4.2.6.2}{Coordination number}{subsection.4.2.6}
\BOOKMARK [3][-]{subsubsection.4.2.6.3}{Spatial Density}{subsection.4.2.6}
\BOOKMARK [3][-]{subsubsection.4.2.6.4}{ScrewFit analysis}{subsection.4.2.6}
\BOOKMARK [2][-]{subsection.4.2.7}{The NMR menu}{section.4.2}
\BOOKMARK [3][-]{subsubsection.4.2.7.1}{Order Parameter}{subsection.4.2.7}
\BOOKMARK [3][-]{subsubsection.4.2.7.2}{Order Parameter \(Contact Model\)}{subsection.4.2.7}
\BOOKMARK [1][-]{section.4.3}{The View menu}{chapter.4}
\BOOKMARK [2][-]{subsection.4.3.1}{Plot}{section.4.3}
\BOOKMARK [2][-]{subsection.4.3.2}{Animation}{section.4.3}
\BOOKMARK [2][-]{subsection.4.3.3}{Effective mode}{section.4.3}
\BOOKMARK [1][-]{section.4.4}{The Help menu}{chapter.4}
\BOOKMARK [2][-]{subsection.4.4.1}{Documentation}{section.4.4}
\BOOKMARK [2][-]{subsection.4.4.2}{Mailing List}{section.4.4}
\BOOKMARK [2][-]{subsection.4.4.3}{API}{section.4.4}
\BOOKMARK [2][-]{subsection.4.4.4}{Analysis benchmark}{section.4.4}
\BOOKMARK [2][-]{subsection.4.4.5}{About nMOLDYN}{section.4.4}
\BOOKMARK [0][-]{chapter.5}{Using nMOLDYN from the command-line interface}{}
\BOOKMARK [1][-]{section.5.1}{nMOLDYN autostart files}{chapter.5}
\BOOKMARK [1][-]{section.5.2}{nMOLDYN input files}{chapter.5}
\BOOKMARK [0][-]{section*.110}{References}{}
\BOOKMARK [0][-]{section*.112}{Appendices}{}
\BOOKMARK [0][-]{Appendix.1.A}{Appendix The FCA algorithm}{}
