\contentsline {section}{\numberline {1}Introduction}{4}
\contentsline {subsection}{\numberline {1.1}Changes from previous versions}{4}
\contentsline {section}{\numberline {2}Description of the molecular structure and the force field}{5}
\contentsline {subsection}{\numberline {2.1}The force field}{5}
\contentsline {subsection}{\numberline {2.2}Molecular geometry and non-bonded interaction parameters}{6}
\contentsline {subsection}{\numberline {2.3}Bonds}{6}
\contentsline {subsection}{\numberline {2.4}Covalent angles}{7}
\contentsline {subsection}{\numberline {2.5}Dihedral angles}{7}
\contentsline {subsection}{\numberline {2.6}Optional features of the force field}{8}
\contentsline {section}{\numberline {3}The main input file}{9}
\contentsline {subsection}{\numberline {3.1}General notes}{9}
\contentsline {subsection}{\numberline {3.2}Basic setup}{10}
\contentsline {subsection}{\numberline {3.3}Restart control}{10}
\contentsline {subsection}{\numberline {3.4}System}{12}
\contentsline {subsection}{\numberline {3.5}Ensemble}{14}
\contentsline {subsection}{\numberline {3.6}Molecular Dynamics}{15}
\contentsline {subsection}{\numberline {3.7}Startup}{16}
\contentsline {subsection}{\numberline {3.8}Expanded Ensemble mode}{18}
\contentsline {subsection}{\numberline {3.9}Path Integral mode}{21}
\contentsline {subsection}{\numberline {3.10}Properties}{21}
\contentsline {section}{\numberline {4}Compilation}{23}
\contentsline {subsection}{\numberline {4.1}Sequential execution}{23}
\contentsline {subsection}{\numberline {4.2}Parallel execution}{24}
\contentsline {subsection}{\numberline {4.3}Other makefiles}{24}
\contentsline {section}{\numberline {5}Execution}{24}
\contentsline {subsection}{\numberline {5.1}Files used by the program}{24}
\contentsline {subsection}{\numberline {5.2}Memory considerations}{24}
\contentsline {subsection}{\numberline {5.3}Program structure}{25}
\contentsline {section}{\numberline {6}{\em Makemol} utility}{26}
\contentsline {subsection}{\numberline {6.1}General organization}{26}
\contentsline {subsection}{\numberline {6.2}The force field (.ff) file}{27}
\contentsline {subsection}{\numberline {6.3}The molecular structure (.smol) file}{28}
\contentsline {section}{\numberline {7}{\em Tranal} utility}{28}
\contentsline {subsection}{\numberline {7.1}General organization}{28}
\contentsline {subsection}{\numberline {7.2}tranal\_base: reading trajectories}{30}
\contentsline {subsection}{\numberline {7.3}Computation of the electron density and electrostatic potential in bilayers: bileldens.f}{32}
\contentsline {subsection}{\numberline {7.4}Dielectric constant: diel.f}{34}
\contentsline {subsection}{\numberline {7.5}Diffusion: diffus.f}{34}
\contentsline {subsection}{\numberline {7.6}Dryrun: dryrun.f}{36}
\contentsline {subsection}{\numberline {7.7}Lateral diffusion: latdiff.f}{36}
\contentsline {subsection}{\numberline {7.8}Order parameters: order.f}{36}
\contentsline {subsection}{\numberline {7.9}Radial distribution functions: rdf.f}{38}
\contentsline {subsection}{\numberline {7.10}Spatial distribution functions: sdf.f}{39}
\contentsline {subsection}{\numberline {7.11}Distribution of torsion angles: torsion.f}{41}
\contentsline {subsection}{\numberline {7.12}Ramachandran plot for a pair of torsion angles: torsion2.f}{42}
\contentsline {subsection}{\numberline {7.13}Residence time calculation: restime.f}{42}
\contentsline {subsection}{\numberline {7.14}Time correlation functions: trtcf.f}{44}
