\contentsline {chapter}{\numberline {1}Introduction}{6}
\contentsline {section}{\numberline {1.1}Useful Features}{6}
\contentsline {subsection}{\numberline {1.1.1}Compatibility with two versions of CHARMM}{6}
\contentsline {subsection}{\numberline {1.1.2}Force field}{6}
\contentsline {subsection}{\numberline {1.1.3}Multiple time-stepping}{7}
\contentsline {subsection}{\numberline {1.1.4}Fast electrostatic computations}{7}
\contentsline {subsection}{\numberline {1.1.5}Comparison of force algorithms}{7}
\contentsline {subsection}{\numberline {1.1.6}Hybrid Monte Carlo sampling}{7}
\contentsline {subsection}{\numberline {1.1.7}Ability to interact with VMD}{7}
\contentsline {subsection}{\numberline {1.1.8}Ability to run on parallel machines}{7}
\contentsline {chapter}{\numberline {2}Getting Started}{8}
\contentsline {section}{\numberline {2.1}Command Line}{8}
\contentsline {subsection}{\numberline {2.1.1}Help Option}{8}
\contentsline {subsection}{\numberline {2.1.2}Man Option}{9}
\contentsline {subsection}{\numberline {2.1.3}Version Option}{9}
\contentsline {subsection}{\numberline {2.1.4}Force Option}{9}
\contentsline {subsection}{\numberline {2.1.5}Constant Option}{9}
\contentsline {subsection}{\numberline {2.1.6}Integrator Option}{10}
\contentsline {subsection}{\numberline {2.1.7}Output Option}{10}
\contentsline {subsection}{\numberline {2.1.8}Topology Option}{10}
\contentsline {subsection}{\numberline {2.1.9}Keyword Option}{10}
\contentsline {subsection}{\numberline {2.1.10}Units Option}{10}
\contentsline {section}{\numberline {2.2}Configuration File}{10}
\contentsline {subsection}{\numberline {2.2.1}Format of \textsc {ProtoMol }keywords in the configuration file}{11}
\contentsline {subsection}{\numberline {2.2.2}Format of the integrator and their arguments}{11}
\contentsline {subsubsection}{Integrator Types}{12}
\contentsline {subsubsection}{Integrator Argument Types}{13}
\contentsline {subsubsection}{General Format of Integrator Forces}{14}
\contentsline {subsubsection}{Force Comparison and Timing}{14}
\contentsline {subsection}{\numberline {2.2.3}Format of forces and their arguments}{16}
\contentsline {subsection}{\numberline {2.2.4}Sample Three-Level Multiple Time-Stepping Integration Scheme}{20}
\contentsline {subsection}{\numberline {2.2.5}Sample of Force Comparison between PME and plain Ewald}{20}
\contentsline {subsection}{\numberline {2.2.6}Sample of Force Comparison and Benchmarking PME with Different Accuracy}{21}
\contentsline {subsection}{\numberline {2.2.7}\textsc {ProtoMol }keywords and descriptions}{22}
\contentsline {section}{\numberline {2.3}Required Parameters}{27}
\contentsline {chapter}{\numberline {3}Input and Output File Types and Formats}{28}
\contentsline {section}{\numberline {3.1}Supported File Formats}{28}
\contentsline {subsection}{\numberline {3.1.1}PDB}{28}
\contentsline {subsection}{\numberline {3.1.2}XYZ}{28}
\contentsline {subsection}{\numberline {3.1.3}PSF}{28}
\contentsline {subsection}{\numberline {3.1.4}CHARMM Parameter Files: New and Old Versions}{29}
\contentsline {subsection}{\numberline {3.1.5}DCD Trajectory Files}{29}
\contentsline {subsection}{\numberline {3.1.6}\textsc {ProtoMol }All Energy Output File }{29}
\contentsline {subsection}{\numberline {3.1.7}\textsc {ProtoMol }Split Energy Output File}{30}
\contentsline {subsection}{\numberline {3.1.8}BSDL File}{30}
\contentsline {subsection}{\numberline {3.1.9}User Specific Output}{30}
\contentsline {section}{\numberline {3.2}Input Files}{30}
\contentsline {section}{\numberline {3.3}Restart Output Files}{30}
\contentsline {section}{\numberline {3.4}User-Specified Output Files}{31}
\contentsline {section}{\numberline {3.5}\textsc {ProtoMol }Units}{31}
\contentsline {section}{\numberline {3.6}Output of Force Comparison}{31}
\contentsline {chapter}{\numberline {4}\textsc {ProtoMol }Configuration Files and Test Molecule Examples}{33}
\contentsline {section}{\numberline {4.1}Alanin Configuration File with Leapfrog Integrator}{33}
\contentsline {section}{\numberline {4.2}20 \r A{ }diameter water droplet With A Two-Level Integration Scheme}{35}
\contentsline {section}{\numberline {4.3}BPTI with Hybrid Monte Carlo Sampling}{37}
\contentsline {chapter}{\numberline {5}Parallelization}{39}
\contentsline {chapter}{\numberline {6}Interaction of \textsc {ProtoMol }with VMD}{40}
\contentsline {chapter}{\numberline {7}Availability and Installation of \textsc {ProtoMol }}{42}
\contentsline {section}{\numberline {7.1}How to Download \textsc {ProtoMol }}{42}
\contentsline {section}{\numberline {7.2}Platforms that \textsc {ProtoMol }is Able to Run On}{42}
\contentsline {section}{\numberline {7.3}Compiling \textsc {ProtoMol }}{42}
\contentsline {section}{\numberline {7.4}Documentation}{43}
\contentsline {chapter}{\numberline {8}The Future of \textsc {ProtoMol }}{44}
\contentsline {chapter}{\numberline {A}Background}{45}
\contentsline {section}{\numberline {A.1}Integrators}{45}
\contentsline {subsection}{\numberline {A.1.1}Standard integrators in \textsc {ProtoMol }}{45}
\contentsline {subsection}{\numberline {A.1.2}Distinction between multiple-time-stepping (MTS) and single-time-stepping (STS) integrators}{45}
\contentsline {subsection}{\numberline {A.1.3}The Verlet-I/r-RESPA Impulse Method \nobreakspace {}\cite {Izag99}}{46}
\contentsline {subsection}{\numberline {A.1.4}Mollified Impulse Methods (\textsc {MOLLY\ }) \nobreakspace {}\cite {Izag99}}{46}
\contentsline {section}{\numberline {A.2}Forces}{48}
\contentsline {subsection}{\numberline {A.2.1}Bond force}{48}
\contentsline {subsection}{\numberline {A.2.2}Angle force}{49}
\contentsline {subsection}{\numberline {A.2.3}Dihedral and improper forces}{49}
\contentsline {subsection}{\numberline {A.2.4}Non-bonded forces}{50}
\contentsline {paragraph}{van der Waals forces\nobreakspace {}\cite {EnBr00}}{51}
\contentsline {paragraph}{Coulomb force\nobreakspace {}\cite {EnBr00}}{51}
\contentsline {section}{\numberline {A.3}Switching Functions}{52}
\contentsline {section}{\numberline {A.4}Boundary Conditions}{52}
\contentsline {section}{\numberline {A.5}Cell Manager}{52}
\contentsline {chapter}{\numberline {B}\textsc {ProtoMol }Molecular Dynamcis Software License}{54}
\contentsline {section}{\numberline {B.1}Conditions and Regulations}{54}
\contentsline {section}{\numberline {B.2}Contact Information}{59}