\relax 
\providecommand\babel@aux[2]{}
\@nameuse{bbl@beforestart}
\providecommand\hyper@newdestlabel[2]{}
\providecommand\HyField@AuxAddToFields[1]{}
\providecommand\HyField@AuxAddToCoFields[2]{}
\babel@aux{english}{}
\newlabel{index::doc}{{}{1}{}{section*.2}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {1}Introduction to the Software}{1}{chapter.1}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/introduction:introduction-to-the-software}{{1}{1}{Introduction to the Software}{chapter.1}{}}
\newlabel{text/introduction::doc}{{1}{1}{Introduction to the Software}{chapter.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {1.1}What is Tinker?}{1}{section.1.1}\protected@file@percent }
\newlabel{text/introduction:what-is-tinker}{{1.1}{1}{What is Tinker?}{section.1.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {1.2}Features and Capabilities}{1}{section.1.2}\protected@file@percent }
\newlabel{text/introduction:features-and-capabilities}{{1.2}{1}{Features and Capabilities}{section.1.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {1.3}Contact Information}{3}{section.1.3}\protected@file@percent }
\newlabel{text/introduction:contact-information}{{1.3}{3}{Contact Information}{section.1.3}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {2}Installation on Your Computer}{5}{chapter.2}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/installation:installation-on-your-computer}{{2}{5}{Installation on Your Computer}{chapter.2}{}}
\newlabel{text/installation::doc}{{2}{5}{Installation on Your Computer}{chapter.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.1}How to Obtain a Copy of Tinker}{5}{section.2.1}\protected@file@percent }
\newlabel{text/installation:how-to-obtain-a-copy-of-tinker}{{2.1}{5}{How to Obtain a Copy of Tinker}{section.2.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.2}Prebuilt Tinker Executables}{5}{section.2.2}\protected@file@percent }
\newlabel{text/installation:prebuilt-tinker-executables}{{2.2}{5}{Prebuilt Tinker Executables}{section.2.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.3}Building your Own Executables}{5}{section.2.3}\protected@file@percent }
\newlabel{text/installation:building-your-own-executables}{{2.3}{5}{Building your Own Executables}{section.2.3}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.4}Tinker\sphinxhyphen {}FFE (Force Field Explorer)}{6}{section.2.4}\protected@file@percent }
\newlabel{text/installation:tinker-ffe-force-field-explorer}{{2.4}{6}{Tinker\sphinxhyphen {}FFE (Force Field Explorer)}{section.2.4}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.5}Documentation and Other Information}{7}{section.2.5}\protected@file@percent }
\newlabel{text/installation:documentation-and-other-information}{{2.5}{7}{Documentation and Other Information}{section.2.5}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.6}Where to Direct Questions and Comments}{7}{section.2.6}\protected@file@percent }
\newlabel{text/installation:where-to-direct-questions-and-comments}{{2.6}{7}{Where to Direct Questions and Comments}{section.2.6}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {3}Types of Input \& Output Files}{9}{chapter.3}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/file-types:types-of-input-output-files}{{3}{9}{Types of Input \& Output Files}{chapter.3}{}}
\newlabel{text/file-types::doc}{{3}{9}{Types of Input \& Output Files}{chapter.3}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {4}Potential Energy Programs}{13}{chapter.4}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/energy-programs:potential-energy-programs}{{4}{13}{Potential Energy Programs}{chapter.4}{}}
\newlabel{text/energy-programs::doc}{{4}{13}{Potential Energy Programs}{chapter.4}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {5}Analysis \& Utility Programs \& Scripts}{21}{chapter.5}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/analysis-programs:analysis-utility-programs-scripts}{{5}{21}{Analysis \& Utility Programs \& Scripts}{chapter.5}{}}
\newlabel{text/analysis-programs::doc}{{5}{21}{Analysis \& Utility Programs \& Scripts}{chapter.5}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {6}Force Field Parameter Sets}{27}{chapter.6}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/parameters:force-field-parameter-sets}{{6}{27}{Force Field Parameter Sets}{chapter.6}{}}
\newlabel{text/parameters::doc}{{6}{27}{Force Field Parameter Sets}{chapter.6}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {7}Special Features \& Methods}{41}{chapter.7}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/special-features:special-features-methods}{{7}{41}{Special Features \& Methods}{chapter.7}{}}
\newlabel{text/special-features::doc}{{7}{41}{Special Features \& Methods}{chapter.7}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.1}File Version Numbers}{41}{section.7.1}\protected@file@percent }
\newlabel{text/special-features:file-version-numbers}{{7.1}{41}{File Version Numbers}{section.7.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.2}Command Line Options}{42}{section.7.2}\protected@file@percent }
\newlabel{text/special-features:command-line-options}{{7.2}{42}{Command Line Options}{section.7.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.3}Use on Windows Systems}{42}{section.7.3}\protected@file@percent }
\newlabel{text/special-features:use-on-windows-systems}{{7.3}{42}{Use on Windows Systems}{section.7.3}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.4}Use on MacOS Systems}{43}{section.7.4}\protected@file@percent }
\newlabel{text/special-features:use-on-macos-systems}{{7.4}{43}{Use on MacOS Systems}{section.7.4}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.5}Atom Types vs. Atom Classes}{43}{section.7.5}\protected@file@percent }
\newlabel{text/special-features:atom-types-vs-atom-classes}{{7.5}{43}{Atom Types vs. Atom Classes}{section.7.5}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.6}Calculations on Partial Structures}{44}{section.7.6}\protected@file@percent }
\newlabel{text/special-features:calculations-on-partial-structures}{{7.6}{44}{Calculations on Partial Structures}{section.7.6}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.7}Metal Complexes and Hypervalent Species}{44}{section.7.7}\protected@file@percent }
\newlabel{text/special-features:metal-complexes-and-hypervalent-species}{{7.7}{44}{Metal Complexes and Hypervalent Species}{section.7.7}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.8}Neighbor Methods for Nonbonded Terms}{45}{section.7.8}\protected@file@percent }
\newlabel{text/special-features:neighbor-methods-for-nonbonded-terms}{{7.8}{45}{Neighbor Methods for Nonbonded Terms}{section.7.8}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.9}Periodic Boundary Conditions}{45}{section.7.9}\protected@file@percent }
\newlabel{text/special-features:periodic-boundary-conditions}{{7.9}{45}{Periodic Boundary Conditions}{section.7.9}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.10}Distance Cutoffs for Energy Functions}{45}{section.7.10}\protected@file@percent }
\newlabel{text/special-features:distance-cutoffs-for-energy-functions}{{7.10}{45}{Distance Cutoffs for Energy Functions}{section.7.10}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.11}Ewald Summations Methods}{45}{section.7.11}\protected@file@percent }
\newlabel{text/special-features:ewald-summations-methods}{{7.11}{45}{Ewald Summations Methods}{section.7.11}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.12}Continuum Solvation Models}{46}{section.7.12}\protected@file@percent }
\newlabel{text/special-features:continuum-solvation-models}{{7.12}{46}{Continuum Solvation Models}{section.7.12}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.13}Polarizable Multipole Electrostatics}{46}{section.7.13}\protected@file@percent }
\newlabel{text/special-features:polarizable-multipole-electrostatics}{{7.13}{46}{Polarizable Multipole Electrostatics}{section.7.13}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.14}Potential Energy Smoothing}{47}{section.7.14}\protected@file@percent }
\newlabel{text/special-features:potential-energy-smoothing}{{7.14}{47}{Potential Energy Smoothing}{section.7.14}{}}
\@writefile{toc}{\contentsline {section}{\numberline {7.15}Distance Geometry Metrization}{47}{section.7.15}\protected@file@percent }
\newlabel{text/special-features:distance-geometry-metrization}{{7.15}{47}{Distance Geometry Metrization}{section.7.15}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {8}Use of the Keyword Control File}{49}{chapter.8}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/keywords:use-of-the-keyword-control-file}{{8}{49}{Use of the Keyword Control File}{chapter.8}{}}
\newlabel{text/keywords::doc}{{8}{49}{Use of the Keyword Control File}{chapter.8}{}}
\@writefile{toc}{\contentsline {section}{\numberline {8.1}Using Keywords to Control Tinker Calculations}{49}{section.8.1}\protected@file@percent }
\newlabel{text/keywords:using-keywords-to-control-tinker-calculations}{{8.1}{49}{Using Keywords to Control Tinker Calculations}{section.8.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {8.2}Keywords Grouped by Functionality}{50}{section.8.2}\protected@file@percent }
\newlabel{text/keywords:keywords-grouped-by-functionality}{{8.2}{50}{Keywords Grouped by Functionality}{section.8.2}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.1}COMPUTER CONTROL KEYWORDS}{50}{subsection.8.2.1}\protected@file@percent }
\newlabel{text/keywords:computer-control-keywords}{{8.2.1}{50}{COMPUTER CONTROL KEYWORDS}{subsection.8.2.1}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.2}OUTPUT CONTROL KEYWORDS}{50}{subsection.8.2.2}\protected@file@percent }
\newlabel{text/keywords:output-control-keywords}{{8.2.2}{50}{OUTPUT CONTROL KEYWORDS}{subsection.8.2.2}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.3}FORCE FIELD SELECTION KEYWORDS}{50}{subsection.8.2.3}\protected@file@percent }
\newlabel{text/keywords:force-field-selection-keywords}{{8.2.3}{50}{FORCE FIELD SELECTION KEYWORDS}{subsection.8.2.3}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.4}POTENTIAL FUNCTION SELECTION KEYWORDS}{50}{subsection.8.2.4}\protected@file@percent }
\newlabel{text/keywords:potential-function-selection-keywords}{{8.2.4}{50}{POTENTIAL FUNCTION SELECTION KEYWORDS}{subsection.8.2.4}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.5}POTENTIAL FUNCTION ENERGY UNIT KEYWORDS}{51}{subsection.8.2.5}\protected@file@percent }
\newlabel{text/keywords:potential-function-energy-unit-keywords}{{8.2.5}{51}{POTENTIAL FUNCTION ENERGY UNIT KEYWORDS}{subsection.8.2.5}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.6}POTENTIAL FUNCTION PARAMETER KEYWORDS}{51}{subsection.8.2.6}\protected@file@percent }
\newlabel{text/keywords:potential-function-parameter-keywords}{{8.2.6}{51}{POTENTIAL FUNCTION PARAMETER KEYWORDS}{subsection.8.2.6}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.7}VALENCE GEOMETRY POTENTIAL KEYWORDS}{51}{subsection.8.2.7}\protected@file@percent }
\newlabel{text/keywords:valence-geometry-potential-keywords}{{8.2.7}{51}{VALENCE GEOMETRY POTENTIAL KEYWORDS}{subsection.8.2.7}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.8}VDW AND REPULSION\sphinxhyphen {}DISPERSION POTENTIAL KEYWORDS}{52}{subsection.8.2.8}\protected@file@percent }
\newlabel{text/keywords:vdw-and-repulsion-dispersion-potential-keywords}{{8.2.8}{52}{VDW AND REPULSION\sphinxhyphen {}DISPERSION POTENTIAL KEYWORDS}{subsection.8.2.8}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.9}ELECTROSTATICS POTENTIAL KEYWORDS}{52}{subsection.8.2.9}\protected@file@percent }
\newlabel{text/keywords:electrostatics-potential-keywords}{{8.2.9}{52}{ELECTROSTATICS POTENTIAL KEYWORDS}{subsection.8.2.9}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.10}NONBONDED CUTOFF KEYWORDS}{52}{subsection.8.2.10}\protected@file@percent }
\newlabel{text/keywords:nonbonded-cutoff-keywords}{{8.2.10}{52}{NONBONDED CUTOFF KEYWORDS}{subsection.8.2.10}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.11}CONSTRAINT AND RESTRAINT KEYWORDS}{53}{subsection.8.2.11}\protected@file@percent }
\newlabel{text/keywords:constraint-and-restraint-keywords}{{8.2.11}{53}{CONSTRAINT AND RESTRAINT KEYWORDS}{subsection.8.2.11}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.12}PARTIAL STRUCTURE KEYWORDS}{53}{subsection.8.2.12}\protected@file@percent }
\newlabel{text/keywords:partial-structure-keywords}{{8.2.12}{53}{PARTIAL STRUCTURE KEYWORDS}{subsection.8.2.12}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.13}NEIGHBOR LIST KEYWORDS}{53}{subsection.8.2.13}\protected@file@percent }
\newlabel{text/keywords:neighbor-list-keywords}{{8.2.13}{53}{NEIGHBOR LIST KEYWORDS}{subsection.8.2.13}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.14}EWALD SUMMATION KEYWORDS}{53}{subsection.8.2.14}\protected@file@percent }
\newlabel{text/keywords:ewald-summation-keywords}{{8.2.14}{53}{EWALD SUMMATION KEYWORDS}{subsection.8.2.14}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.15}CRYSTAL LATTICE AND PERIODIC BOUNDARY KEYWORDS}{53}{subsection.8.2.15}\protected@file@percent }
\newlabel{text/keywords:crystal-lattice-and-periodic-boundary-keywords}{{8.2.15}{53}{CRYSTAL LATTICE AND PERIODIC BOUNDARY KEYWORDS}{subsection.8.2.15}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.16}MATHEMATICAL METHODS KEYWORDS}{54}{subsection.8.2.16}\protected@file@percent }
\newlabel{text/keywords:mathematical-methods-keywords}{{8.2.16}{54}{MATHEMATICAL METHODS KEYWORDS}{subsection.8.2.16}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.17}OPTIMIZATION KEYWORDS}{54}{subsection.8.2.17}\protected@file@percent }
\newlabel{text/keywords:optimization-keywords}{{8.2.17}{54}{OPTIMIZATION KEYWORDS}{subsection.8.2.17}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.18}MOLECULAR AND STOCHASTIC DYNAMICS KEYWORDS}{54}{subsection.8.2.18}\protected@file@percent }
\newlabel{text/keywords:molecular-and-stochastic-dynamics-keywords}{{8.2.18}{54}{MOLECULAR AND STOCHASTIC DYNAMICS KEYWORDS}{subsection.8.2.18}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.19}THERMOSTAT AND BAROSTAT KEYWORDS}{54}{subsection.8.2.19}\protected@file@percent }
\newlabel{text/keywords:thermostat-and-barostat-keywords}{{8.2.19}{54}{THERMOSTAT AND BAROSTAT KEYWORDS}{subsection.8.2.19}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.20}SURFACE AREA AND VOLUME KEYWORDS}{54}{subsection.8.2.20}\protected@file@percent }
\newlabel{text/keywords:surface-area-and-volume-keywords}{{8.2.20}{54}{SURFACE AREA AND VOLUME KEYWORDS}{subsection.8.2.20}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.21}IMPLICIT SOLVATION KEYWORDS}{55}{subsection.8.2.21}\protected@file@percent }
\newlabel{text/keywords:implicit-solvation-keywords}{{8.2.21}{55}{IMPLICIT SOLVATION KEYWORDS}{subsection.8.2.21}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.22}POISSON\sphinxhyphen {}BOLTZMANN KEYWORDS}{55}{subsection.8.2.22}\protected@file@percent }
\newlabel{text/keywords:poisson-boltzmann-keywords}{{8.2.22}{55}{POISSON\sphinxhyphen {}BOLTZMANN KEYWORDS}{subsection.8.2.22}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.23}TRANSITION STATE KEYWORDS}{55}{subsection.8.2.23}\protected@file@percent }
\newlabel{text/keywords:transition-state-keywords}{{8.2.23}{55}{TRANSITION STATE KEYWORDS}{subsection.8.2.23}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.24}DISTANCE GEOMETRY KEYWORDS}{55}{subsection.8.2.24}\protected@file@percent }
\newlabel{text/keywords:distance-geometry-keywords}{{8.2.24}{55}{DISTANCE GEOMETRY KEYWORDS}{subsection.8.2.24}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.25}VIBRATIONAL ANALYSIS KEYWORDS}{55}{subsection.8.2.25}\protected@file@percent }
\newlabel{text/keywords:vibrational-analysis-keywords}{{8.2.25}{55}{VIBRATIONAL ANALYSIS KEYWORDS}{subsection.8.2.25}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.26}FREE ENERGY PERTURBATION KEYWORDS}{56}{subsection.8.2.26}\protected@file@percent }
\newlabel{text/keywords:free-energy-perturbation-keywords}{{8.2.26}{56}{FREE ENERGY PERTURBATION KEYWORDS}{subsection.8.2.26}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.27}POTENTIAL SMOOTHING KEYWORDS}{56}{subsection.8.2.27}\protected@file@percent }
\newlabel{text/keywords:potential-smoothing-keywords}{{8.2.27}{56}{POTENTIAL SMOOTHING KEYWORDS}{subsection.8.2.27}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.28}VALENCE PARAMETER FITTING KEYWORDS}{56}{subsection.8.2.28}\protected@file@percent }
\newlabel{text/keywords:valence-parameter-fitting-keywords}{{8.2.28}{56}{VALENCE PARAMETER FITTING KEYWORDS}{subsection.8.2.28}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {8.2.29}ELECTROSTATIC POTENTIAL FITTING KEYWORDS}{56}{subsection.8.2.29}\protected@file@percent }
\newlabel{text/keywords:electrostatic-potential-fitting-keywords}{{8.2.29}{56}{ELECTROSTATIC POTENTIAL FITTING KEYWORDS}{subsection.8.2.29}{}}
\@writefile{toc}{\contentsline {section}{\numberline {8.3}Description of Individual Keywords}{56}{section.8.3}\protected@file@percent }
\newlabel{text/keywords:description-of-individual-keywords}{{8.3}{56}{Description of Individual Keywords}{section.8.3}{}}
\newlabel{text/keywords:key-a-axis}{{8.3}{56}{Description of Individual Keywords}{section*.3}{}}
\newlabel{text/keywords:key-a-expterm}{{8.3}{56}{Description of Individual Keywords}{section*.4}{}}
\newlabel{text/keywords:key-active}{{8.3}{56}{Description of Individual Keywords}{section*.5}{}}
\newlabel{text/keywords:key-active-sphere}{{8.3}{57}{Description of Individual Keywords}{section*.6}{}}
\newlabel{text/keywords:key-alf-method}{{8.3}{57}{Description of Individual Keywords}{section*.7}{}}
\newlabel{text/keywords:key-alf-nohydro}{{8.3}{57}{Description of Individual Keywords}{section*.8}{}}
\newlabel{text/keywords:key-alf-sort}{{8.3}{57}{Description of Individual Keywords}{section*.9}{}}
\newlabel{text/keywords:key-alf-sosgmp}{{8.3}{57}{Description of Individual Keywords}{section*.10}{}}
\newlabel{text/keywords:key-alpha}{{8.3}{57}{Description of Individual Keywords}{section*.11}{}}
\newlabel{text/keywords:key-angang}{{8.3}{57}{Description of Individual Keywords}{section*.12}{}}
\newlabel{text/keywords:key-angangterm}{{8.3}{58}{Description of Individual Keywords}{section*.13}{}}
\newlabel{text/keywords:key-angangunit}{{8.3}{58}{Description of Individual Keywords}{section*.14}{}}
\newlabel{text/keywords:key-angcflux}{{8.3}{58}{Description of Individual Keywords}{section*.15}{}}
\newlabel{text/keywords:key-angle}{{8.3}{58}{Description of Individual Keywords}{section*.16}{}}
\newlabel{text/keywords:key-angle-cubic}{{8.3}{58}{Description of Individual Keywords}{section*.17}{}}
\newlabel{text/keywords:key-angle-pentic}{{8.3}{58}{Description of Individual Keywords}{section*.18}{}}
\newlabel{text/keywords:key-angle-quartic}{{8.3}{59}{Description of Individual Keywords}{section*.19}{}}
\newlabel{text/keywords:key-angle-sextic}{{8.3}{59}{Description of Individual Keywords}{section*.20}{}}
\newlabel{text/keywords:key-angle3}{{8.3}{59}{Description of Individual Keywords}{section*.21}{}}
\newlabel{text/keywords:key-angle4}{{8.3}{59}{Description of Individual Keywords}{section*.22}{}}
\newlabel{text/keywords:key-angle5}{{8.3}{59}{Description of Individual Keywords}{section*.23}{}}
\newlabel{text/keywords:key-anglef}{{8.3}{60}{Description of Individual Keywords}{section*.24}{}}
\newlabel{text/keywords:key-anglep}{{8.3}{60}{Description of Individual Keywords}{section*.25}{}}
\newlabel{text/keywords:key-angleterm}{{8.3}{60}{Description of Individual Keywords}{section*.26}{}}
\newlabel{text/keywords:key-angleunit}{{8.3}{60}{Description of Individual Keywords}{section*.27}{}}
\newlabel{text/keywords:key-angmax}{{8.3}{60}{Description of Individual Keywords}{section*.28}{}}
\newlabel{text/keywords:key-angtors}{{8.3}{61}{Description of Individual Keywords}{section*.29}{}}
\newlabel{text/keywords:key-angtorterm}{{8.3}{61}{Description of Individual Keywords}{section*.30}{}}
\newlabel{text/keywords:key-angtorunit}{{8.3}{61}{Description of Individual Keywords}{section*.31}{}}
\newlabel{text/keywords:key-apbs-agrid}{{8.3}{61}{Description of Individual Keywords}{section*.32}{}}
\newlabel{text/keywords:key-apbs-bcfl}{{8.3}{61}{Description of Individual Keywords}{section*.33}{}}
\newlabel{text/keywords:key-apbs-cgcent}{{8.3}{61}{Description of Individual Keywords}{section*.34}{}}
\newlabel{text/keywords:key-apbs-cgrid}{{8.3}{61}{Description of Individual Keywords}{section*.35}{}}
\newlabel{text/keywords:key-apbs-dime}{{8.3}{61}{Description of Individual Keywords}{section*.36}{}}
\newlabel{text/keywords:key-apbs-chgm}{{8.3}{61}{Description of Individual Keywords}{section*.37}{}}
\newlabel{text/keywords:key-apbs-fgcent}{{8.3}{61}{Description of Individual Keywords}{section*.38}{}}
\newlabel{text/keywords:key-apbs-fgrid}{{8.3}{62}{Description of Individual Keywords}{section*.39}{}}
\newlabel{text/keywords:key-apbs-gcent}{{8.3}{62}{Description of Individual Keywords}{section*.40}{}}
\newlabel{text/keywords:key-apbs-grid}{{8.3}{62}{Description of Individual Keywords}{section*.41}{}}
\newlabel{text/keywords:key-apbs-ion}{{8.3}{62}{Description of Individual Keywords}{section*.42}{}}
\newlabel{text/keywords:key-apbs-mg-auto}{{8.3}{62}{Description of Individual Keywords}{section*.43}{}}
\newlabel{text/keywords:key-apbs-mg-manual}{{8.3}{62}{Description of Individual Keywords}{section*.44}{}}
\newlabel{text/keywords:key-apbs-pdie}{{8.3}{62}{Description of Individual Keywords}{section*.45}{}}
\newlabel{text/keywords:key-apbs-radii}{{8.3}{62}{Description of Individual Keywords}{section*.46}{}}
\newlabel{text/keywords:key-apbs-sdens}{{8.3}{62}{Description of Individual Keywords}{section*.47}{}}
\newlabel{text/keywords:key-apbs-sdie}{{8.3}{62}{Description of Individual Keywords}{section*.48}{}}
\newlabel{text/keywords:key-apbs-smin}{{8.3}{63}{Description of Individual Keywords}{section*.49}{}}
\newlabel{text/keywords:key-apbs-srad}{{8.3}{63}{Description of Individual Keywords}{section*.50}{}}
\newlabel{text/keywords:key-apbs-srfm}{{8.3}{63}{Description of Individual Keywords}{section*.51}{}}
\newlabel{text/keywords:key-apbs-swin}{{8.3}{63}{Description of Individual Keywords}{section*.52}{}}
\newlabel{text/keywords:key-archive}{{8.3}{63}{Description of Individual Keywords}{section*.53}{}}
\newlabel{text/keywords:key-atom}{{8.3}{63}{Description of Individual Keywords}{section*.54}{}}
\newlabel{text/keywords:key-aux-tautemp}{{8.3}{63}{Description of Individual Keywords}{section*.55}{}}
\newlabel{text/keywords:key-aux-temp}{{8.3}{63}{Description of Individual Keywords}{section*.56}{}}
\newlabel{text/keywords:key-b-axis}{{8.3}{64}{Description of Individual Keywords}{section*.57}{}}
\newlabel{text/keywords:key-b-expterm}{{8.3}{64}{Description of Individual Keywords}{section*.58}{}}
\newlabel{text/keywords:key-barostat}{{8.3}{64}{Description of Individual Keywords}{section*.59}{}}
\newlabel{text/keywords:key-basin}{{8.3}{64}{Description of Individual Keywords}{section*.60}{}}
\newlabel{text/keywords:key-beeman-mixing}{{8.3}{64}{Description of Individual Keywords}{section*.61}{}}
\newlabel{text/keywords:key-beta}{{8.3}{64}{Description of Individual Keywords}{section*.62}{}}
\newlabel{text/keywords:key-biotype}{{8.3}{64}{Description of Individual Keywords}{section*.63}{}}
\newlabel{text/keywords:key-bond}{{8.3}{64}{Description of Individual Keywords}{section*.64}{}}
\newlabel{text/keywords:key-bond-cubic}{{8.3}{64}{Description of Individual Keywords}{section*.65}{}}
\newlabel{text/keywords:key-bond-quartic}{{8.3}{65}{Description of Individual Keywords}{section*.66}{}}
\newlabel{text/keywords:key-bond3}{{8.3}{65}{Description of Individual Keywords}{section*.67}{}}
\newlabel{text/keywords:key-bond4}{{8.3}{65}{Description of Individual Keywords}{section*.68}{}}
\newlabel{text/keywords:key-bond5}{{8.3}{65}{Description of Individual Keywords}{section*.69}{}}
\newlabel{text/keywords:key-bondterm}{{8.3}{65}{Description of Individual Keywords}{section*.70}{}}
\newlabel{text/keywords:key-bondtype}{{8.3}{66}{Description of Individual Keywords}{section*.71}{}}
\newlabel{text/keywords:key-bondunit}{{8.3}{66}{Description of Individual Keywords}{section*.72}{}}
\newlabel{text/keywords:key-born-radius}{{8.3}{66}{Description of Individual Keywords}{section*.73}{}}
\newlabel{text/keywords:key-c-axis}{{8.3}{66}{Description of Individual Keywords}{section*.74}{}}
\newlabel{text/keywords:key-c-expterm}{{8.3}{66}{Description of Individual Keywords}{section*.75}{}}
\newlabel{text/keywords:key-cappa}{{8.3}{66}{Description of Individual Keywords}{section*.76}{}}
\newlabel{text/keywords:key-cavity-probe}{{8.3}{66}{Description of Individual Keywords}{section*.77}{}}
\newlabel{text/keywords:key-charge}{{8.3}{66}{Description of Individual Keywords}{section*.78}{}}
\newlabel{text/keywords:key-charge-cutoff}{{8.3}{66}{Description of Individual Keywords}{section*.79}{}}
\newlabel{text/keywords:key-charge-list}{{8.3}{67}{Description of Individual Keywords}{section*.80}{}}
\newlabel{text/keywords:key-charge-taper}{{8.3}{67}{Description of Individual Keywords}{section*.81}{}}
\newlabel{text/keywords:key-chargeterm}{{8.3}{67}{Description of Individual Keywords}{section*.82}{}}
\newlabel{text/keywords:key-chargetransfer}{{8.3}{67}{Description of Individual Keywords}{section*.83}{}}
\newlabel{text/keywords:key-chg-11-scale}{{8.3}{67}{Description of Individual Keywords}{section*.84}{}}
\newlabel{text/keywords:key-chg-12-scale}{{8.3}{67}{Description of Individual Keywords}{section*.85}{}}
\newlabel{text/keywords:key-chg-13-scale}{{8.3}{67}{Description of Individual Keywords}{section*.86}{}}
\newlabel{text/keywords:key-chg-14-scale}{{8.3}{67}{Description of Individual Keywords}{section*.87}{}}
\newlabel{text/keywords:key-chg-15-scale}{{8.3}{68}{Description of Individual Keywords}{section*.88}{}}
\newlabel{text/keywords:key-chg-buffer}{{8.3}{68}{Description of Individual Keywords}{section*.89}{}}
\newlabel{text/keywords:key-chgdplterm}{{8.3}{68}{Description of Individual Keywords}{section*.90}{}}
\newlabel{text/keywords:key-chgflxterm}{{8.3}{68}{Description of Individual Keywords}{section*.91}{}}
\newlabel{text/keywords:key-chgpen}{{8.3}{68}{Description of Individual Keywords}{section*.92}{}}
\newlabel{text/keywords:key-chgtrn}{{8.3}{68}{Description of Individual Keywords}{section*.93}{}}
\newlabel{text/keywords:key-chgtrn-cutoff}{{8.3}{68}{Description of Individual Keywords}{section*.94}{}}
\newlabel{text/keywords:key-chgtrn-taper}{{8.3}{68}{Description of Individual Keywords}{section*.95}{}}
\newlabel{text/keywords:key-chgtrnterm}{{8.3}{69}{Description of Individual Keywords}{section*.96}{}}
\newlabel{text/keywords:key-collision}{{8.3}{69}{Description of Individual Keywords}{section*.97}{}}
\newlabel{text/keywords:key-compress}{{8.3}{69}{Description of Individual Keywords}{section*.98}{}}
\newlabel{text/keywords:key-cuda-device}{{8.3}{69}{Description of Individual Keywords}{section*.99}{}}
\newlabel{text/keywords:key-cutoff}{{8.3}{69}{Description of Individual Keywords}{section*.100}{}}
\newlabel{text/keywords:key-d-equals-p}{{8.3}{69}{Description of Individual Keywords}{section*.101}{}}
\newlabel{text/keywords:key-dcd-archive}{{8.3}{69}{Description of Individual Keywords}{section*.102}{}}
\newlabel{text/keywords:key-debug}{{8.3}{69}{Description of Individual Keywords}{section*.103}{}}
\newlabel{text/keywords:key-deform}{{8.3}{70}{Description of Individual Keywords}{section*.104}{}}
\newlabel{text/keywords:key-degrees-freedom}{{8.3}{70}{Description of Individual Keywords}{section*.105}{}}
\newlabel{text/keywords:key-delcx-eps}{{8.3}{70}{Description of Individual Keywords}{section*.106}{}}
\newlabel{text/keywords:key-delta-halgren}{{8.3}{70}{Description of Individual Keywords}{section*.107}{}}
\newlabel{text/keywords:key-descreen-hydrogen}{{8.3}{70}{Description of Individual Keywords}{section*.108}{}}
\newlabel{text/keywords:key-descreen-offset}{{8.3}{70}{Description of Individual Keywords}{section*.109}{}}
\newlabel{text/keywords:key-dewald}{{8.3}{70}{Description of Individual Keywords}{section*.110}{}}
\newlabel{text/keywords:key-dewald-alpha}{{8.3}{70}{Description of Individual Keywords}{section*.111}{}}
\newlabel{text/keywords:key-dewald-cutoff}{{8.3}{70}{Description of Individual Keywords}{section*.112}{}}
\newlabel{text/keywords:key-dielectric}{{8.3}{70}{Description of Individual Keywords}{section*.113}{}}
\newlabel{text/keywords:key-dielectric-offset}{{8.3}{70}{Description of Individual Keywords}{section*.114}{}}
\newlabel{text/keywords:key-diffuse-charge}{{8.3}{71}{Description of Individual Keywords}{section*.115}{}}
\newlabel{text/keywords:key-diffuse-torsion}{{8.3}{71}{Description of Individual Keywords}{section*.116}{}}
\newlabel{text/keywords:key-diffuse-vdw}{{8.3}{71}{Description of Individual Keywords}{section*.117}{}}
\newlabel{text/keywords:key-digits}{{8.3}{71}{Description of Individual Keywords}{section*.118}{}}
\newlabel{text/keywords:key-dipole}{{8.3}{71}{Description of Individual Keywords}{section*.119}{}}
\newlabel{text/keywords:key-dipole-cutoff}{{8.3}{71}{Description of Individual Keywords}{section*.120}{}}
\newlabel{text/keywords:key-dipole-taper}{{8.3}{71}{Description of Individual Keywords}{section*.121}{}}
\newlabel{text/keywords:key-dipole3}{{8.3}{72}{Description of Individual Keywords}{section*.122}{}}
\newlabel{text/keywords:key-dipole4}{{8.3}{72}{Description of Individual Keywords}{section*.123}{}}
\newlabel{text/keywords:key-dipole5}{{8.3}{72}{Description of Individual Keywords}{section*.124}{}}
\newlabel{text/keywords:key-dipoleterm}{{8.3}{72}{Description of Individual Keywords}{section*.125}{}}
\newlabel{text/keywords:key-direct-11-scale}{{8.3}{72}{Description of Individual Keywords}{section*.126}{}}
\newlabel{text/keywords:key-direct-12-scale}{{8.3}{72}{Description of Individual Keywords}{section*.127}{}}
\newlabel{text/keywords:key-direct-13-scale}{{8.3}{73}{Description of Individual Keywords}{section*.128}{}}
\newlabel{text/keywords:key-direct-14-scale}{{8.3}{73}{Description of Individual Keywords}{section*.129}{}}
\newlabel{text/keywords:key-disp-12-scale}{{8.3}{73}{Description of Individual Keywords}{section*.130}{}}
\newlabel{text/keywords:key-disp-13-scale}{{8.3}{73}{Description of Individual Keywords}{section*.131}{}}
\newlabel{text/keywords:key-disp-14-scale}{{8.3}{73}{Description of Individual Keywords}{section*.132}{}}
\newlabel{text/keywords:key-disp-15-scale}{{8.3}{73}{Description of Individual Keywords}{section*.133}{}}
\newlabel{text/keywords:key-disp-correction}{{8.3}{73}{Description of Individual Keywords}{section*.134}{}}
\newlabel{text/keywords:key-disp-cutoff}{{8.3}{73}{Description of Individual Keywords}{section*.135}{}}
\newlabel{text/keywords:key-disp-list}{{8.3}{73}{Description of Individual Keywords}{section*.136}{}}
\newlabel{text/keywords:key-disp-taper}{{8.3}{74}{Description of Individual Keywords}{section*.137}{}}
\newlabel{text/keywords:key-dispersion}{{8.3}{74}{Description of Individual Keywords}{section*.138}{}}
\newlabel{text/keywords:key-dispersionterm}{{8.3}{74}{Description of Individual Keywords}{section*.139}{}}
\newlabel{text/keywords:key-diverge}{{8.3}{74}{Description of Individual Keywords}{section*.140}{}}
\newlabel{text/keywords:key-dodecahedron}{{8.3}{74}{Description of Individual Keywords}{section*.141}{}}
\newlabel{text/keywords:key-dpme-grid}{{8.3}{74}{Description of Individual Keywords}{section*.142}{}}
\newlabel{text/keywords:key-dpme-order}{{8.3}{74}{Description of Individual Keywords}{section*.143}{}}
\newlabel{text/keywords:key-echo}{{8.3}{74}{Description of Individual Keywords}{section*.144}{}}
\newlabel{text/keywords:key-ele-lambda}{{8.3}{75}{Description of Individual Keywords}{section*.145}{}}
\newlabel{text/keywords:key-electneg}{{8.3}{75}{Description of Individual Keywords}{section*.146}{}}
\newlabel{text/keywords:key-electric}{{8.3}{75}{Description of Individual Keywords}{section*.147}{}}
\newlabel{text/keywords:key-enforce-chirality}{{8.3}{75}{Description of Individual Keywords}{section*.148}{}}
\newlabel{text/keywords:key-epsilonrule}{{8.3}{75}{Description of Individual Keywords}{section*.149}{}}
\newlabel{text/keywords:key-ewald}{{8.3}{75}{Description of Individual Keywords}{section*.150}{}}
\newlabel{text/keywords:key-ewald-alpha}{{8.3}{75}{Description of Individual Keywords}{section*.151}{}}
\newlabel{text/keywords:key-ewald-boundary}{{8.3}{76}{Description of Individual Keywords}{section*.152}{}}
\newlabel{text/keywords:key-ewald-cutoff}{{8.3}{76}{Description of Individual Keywords}{section*.153}{}}
\newlabel{text/keywords:key-exchange-polar}{{8.3}{76}{Description of Individual Keywords}{section*.154}{}}
\newlabel{text/keywords:key-external-field}{{8.3}{76}{Description of Individual Keywords}{section*.155}{}}
\newlabel{text/keywords:key-exchpol}{{8.3}{76}{Description of Individual Keywords}{section*.156}{}}
\newlabel{text/keywords:key-exit-pause}{{8.3}{76}{Description of Individual Keywords}{section*.157}{}}
\newlabel{text/keywords:key-extraterm}{{8.3}{76}{Description of Individual Keywords}{section*.158}{}}
\newlabel{text/keywords:key-fctmin}{{8.3}{76}{Description of Individual Keywords}{section*.159}{}}
\newlabel{text/keywords:key-fft-package}{{8.3}{76}{Description of Individual Keywords}{section*.160}{}}
\newlabel{text/keywords:key-fit-angle}{{8.3}{77}{Description of Individual Keywords}{section*.161}{}}
\newlabel{text/keywords:key-fit-bond}{{8.3}{77}{Description of Individual Keywords}{section*.162}{}}
\newlabel{text/keywords:key-fit-opbend}{{8.3}{77}{Description of Individual Keywords}{section*.163}{}}
\newlabel{text/keywords:key-fit-strbnd}{{8.3}{77}{Description of Individual Keywords}{section*.164}{}}
\newlabel{text/keywords:key-fit-torsion}{{8.3}{77}{Description of Individual Keywords}{section*.165}{}}
\newlabel{text/keywords:key-fit-urey}{{8.3}{77}{Description of Individual Keywords}{section*.166}{}}
\newlabel{text/keywords:key-fix-angle}{{8.3}{77}{Description of Individual Keywords}{section*.167}{}}
\newlabel{text/keywords:key-fix-atom-dipole}{{8.3}{77}{Description of Individual Keywords}{section*.168}{}}
\newlabel{text/keywords:key-fix-bond}{{8.3}{77}{Description of Individual Keywords}{section*.169}{}}
\newlabel{text/keywords:key-fix-chgpen}{{8.3}{77}{Description of Individual Keywords}{section*.170}{}}
\newlabel{text/keywords:key-fix-dipole}{{8.3}{77}{Description of Individual Keywords}{section*.171}{}}
\newlabel{text/keywords:key-fix-monopole}{{8.3}{77}{Description of Individual Keywords}{section*.172}{}}
\newlabel{text/keywords:key-fix-opbend}{{8.3}{77}{Description of Individual Keywords}{section*.173}{}}
\newlabel{text/keywords:key-fix-quadrupole}{{8.3}{77}{Description of Individual Keywords}{section*.174}{}}
\newlabel{text/keywords:key-fix-strbnd}{{8.3}{77}{Description of Individual Keywords}{section*.175}{}}
\newlabel{text/keywords:key-fix-torsion}{{8.3}{77}{Description of Individual Keywords}{section*.176}{}}
\newlabel{text/keywords:key-fix-urey}{{8.3}{77}{Description of Individual Keywords}{section*.177}{}}
\newlabel{text/keywords:key-forcefield}{{8.3}{78}{Description of Individual Keywords}{section*.178}{}}
\newlabel{text/keywords:key-freeze}{{8.3}{78}{Description of Individual Keywords}{section*.179}{}}
\newlabel{text/keywords:key-freeze-distance}{{8.3}{78}{Description of Individual Keywords}{section*.180}{}}
\newlabel{text/keywords:key-freeze-eps}{{8.3}{78}{Description of Individual Keywords}{section*.181}{}}
\newlabel{text/keywords:key-freeze-line}{{8.3}{78}{Description of Individual Keywords}{section*.182}{}}
\newlabel{text/keywords:key-freeze-origin}{{8.3}{78}{Description of Individual Keywords}{section*.183}{}}
\newlabel{text/keywords:key-freeze-plane}{{8.3}{78}{Description of Individual Keywords}{section*.184}{}}
\newlabel{text/keywords:key-reactionfield}{{8.3}{78}{Description of Individual Keywords}{section*.185}{}}
\newlabel{text/keywords:key-friction}{{8.3}{78}{Description of Individual Keywords}{section*.186}{}}
\newlabel{text/keywords:key-friction-scaling}{{8.3}{78}{Description of Individual Keywords}{section*.187}{}}
\newlabel{text/keywords:key-gamma}{{8.3}{78}{Description of Individual Keywords}{section*.188}{}}
\newlabel{text/keywords:key-gamma-halgren}{{8.3}{78}{Description of Individual Keywords}{section*.189}{}}
\newlabel{text/keywords:key-gammamin}{{8.3}{78}{Description of Individual Keywords}{section*.190}{}}
\newlabel{text/keywords:key-gausstype}{{8.3}{79}{Description of Individual Keywords}{section*.191}{}}
\newlabel{text/keywords:key-gk-radius}{{8.3}{79}{Description of Individual Keywords}{section*.192}{}}
\newlabel{text/keywords:key-gkc}{{8.3}{79}{Description of Individual Keywords}{section*.193}{}}
\newlabel{text/keywords:key-gkr}{{8.3}{79}{Description of Individual Keywords}{section*.194}{}}
\newlabel{text/keywords:key-group}{{8.3}{79}{Description of Individual Keywords}{section*.195}{}}
\newlabel{text/keywords:key-group-inter}{{8.3}{79}{Description of Individual Keywords}{section*.196}{}}
\newlabel{text/keywords:key-group-intra}{{8.3}{79}{Description of Individual Keywords}{section*.197}{}}
\newlabel{text/keywords:key-group-molecule}{{8.3}{79}{Description of Individual Keywords}{section*.198}{}}
\newlabel{text/keywords:key-group-select}{{8.3}{79}{Description of Individual Keywords}{section*.199}{}}
\newlabel{text/keywords:key-hbond}{{8.3}{79}{Description of Individual Keywords}{section*.200}{}}
\newlabel{text/keywords:key-hct-element}{{8.3}{80}{Description of Individual Keywords}{section*.201}{}}
\newlabel{text/keywords:key-hct-scale}{{8.3}{80}{Description of Individual Keywords}{section*.202}{}}
\newlabel{text/keywords:key-heavy-hydrogen}{{8.3}{80}{Description of Individual Keywords}{section*.203}{}}
\newlabel{text/keywords:key-hessian-cutoff}{{8.3}{80}{Description of Individual Keywords}{section*.204}{}}
\newlabel{text/keywords:key-hguess}{{8.3}{80}{Description of Individual Keywords}{section*.205}{}}
\newlabel{text/keywords:key-iel-scf}{{8.3}{80}{Description of Individual Keywords}{section*.206}{}}
\newlabel{text/keywords:key-improper}{{8.3}{80}{Description of Individual Keywords}{section*.207}{}}
\newlabel{text/keywords:key-impropterm}{{8.3}{80}{Description of Individual Keywords}{section*.208}{}}
\newlabel{text/keywords:key-impropunit}{{8.3}{80}{Description of Individual Keywords}{section*.209}{}}
\newlabel{text/keywords:key-imptors}{{8.3}{81}{Description of Individual Keywords}{section*.210}{}}
\newlabel{text/keywords:key-imptorsterm}{{8.3}{81}{Description of Individual Keywords}{section*.211}{}}
\newlabel{text/keywords:key-imptorsunit}{{8.3}{81}{Description of Individual Keywords}{section*.212}{}}
\newlabel{text/keywords:key-inactive}{{8.3}{81}{Description of Individual Keywords}{section*.213}{}}
\newlabel{text/keywords:key-induce-12-scale}{{8.3}{81}{Description of Individual Keywords}{section*.214}{}}
\newlabel{text/keywords:key-induce-13-scale}{{8.3}{81}{Description of Individual Keywords}{section*.215}{}}
\newlabel{text/keywords:key-induce-14-scale}{{8.3}{81}{Description of Individual Keywords}{section*.216}{}}
\newlabel{text/keywords:key-induce-15-scale}{{8.3}{82}{Description of Individual Keywords}{section*.217}{}}
\newlabel{text/keywords:key-integrator}{{8.3}{82}{Description of Individual Keywords}{section*.218}{}}
\newlabel{text/keywords:key-intmax}{{8.3}{82}{Description of Individual Keywords}{section*.219}{}}
\newlabel{text/keywords:key-lambda}{{8.3}{82}{Description of Individual Keywords}{section*.220}{}}
\newlabel{text/keywords:key-lbfgs-vectors}{{8.3}{82}{Description of Individual Keywords}{section*.221}{}}
\newlabel{text/keywords:key-ligand}{{8.3}{82}{Description of Individual Keywords}{section*.222}{}}
\newlabel{text/keywords:key-lights}{{8.3}{82}{Description of Individual Keywords}{section*.223}{}}
\newlabel{text/keywords:key-list-buffer}{{8.3}{83}{Description of Individual Keywords}{section*.224}{}}
\newlabel{text/keywords:key-maxiter}{{8.3}{83}{Description of Individual Keywords}{section*.225}{}}
\newlabel{text/keywords:key-metal}{{8.3}{83}{Description of Individual Keywords}{section*.226}{}}
\newlabel{text/keywords:key-metalterm}{{8.3}{83}{Description of Individual Keywords}{section*.227}{}}
\newlabel{text/keywords:key-mmff-pibond}{{8.3}{83}{Description of Individual Keywords}{section*.228}{}}
\newlabel{text/keywords:key-mmffangle}{{8.3}{83}{Description of Individual Keywords}{section*.229}{}}
\newlabel{text/keywords:key-mmffarom}{{8.3}{83}{Description of Individual Keywords}{section*.230}{}}
\newlabel{text/keywords:key-mmffbci}{{8.3}{83}{Description of Individual Keywords}{section*.231}{}}
\newlabel{text/keywords:key-mmffbond}{{8.3}{83}{Description of Individual Keywords}{section*.232}{}}
\newlabel{text/keywords:key-mmffbonder}{{8.3}{83}{Description of Individual Keywords}{section*.233}{}}
\newlabel{text/keywords:key-mmffcovrad}{{8.3}{83}{Description of Individual Keywords}{section*.234}{}}
\newlabel{text/keywords:key-mmffdefstbn}{{8.3}{83}{Description of Individual Keywords}{section*.235}{}}
\newlabel{text/keywords:key-mmffequiv}{{8.3}{83}{Description of Individual Keywords}{section*.236}{}}
\newlabel{text/keywords:key-mmffopbend}{{8.3}{83}{Description of Individual Keywords}{section*.237}{}}
\newlabel{text/keywords:key-mmffpbci}{{8.3}{83}{Description of Individual Keywords}{section*.238}{}}
\newlabel{text/keywords:key-mmffprop}{{8.3}{83}{Description of Individual Keywords}{section*.239}{}}
\newlabel{text/keywords:key-mmffstrbnd}{{8.3}{83}{Description of Individual Keywords}{section*.240}{}}
\newlabel{text/keywords:key-mmfftorsion}{{8.3}{83}{Description of Individual Keywords}{section*.241}{}}
\newlabel{text/keywords:key-mmffvdw}{{8.3}{83}{Description of Individual Keywords}{section*.242}{}}
\newlabel{text/keywords:key-mpole-12-scale}{{8.3}{84}{Description of Individual Keywords}{section*.243}{}}
\newlabel{text/keywords:key-mpole-13-scale}{{8.3}{84}{Description of Individual Keywords}{section*.244}{}}
\newlabel{text/keywords:key-mpole-14-scale}{{8.3}{84}{Description of Individual Keywords}{section*.245}{}}
\newlabel{text/keywords:key-mpole-15-scale}{{8.3}{84}{Description of Individual Keywords}{section*.246}{}}
\newlabel{text/keywords:key-mpole-cutoff}{{8.3}{84}{Description of Individual Keywords}{section*.247}{}}
\newlabel{text/keywords:key-mpole-list}{{8.3}{84}{Description of Individual Keywords}{section*.248}{}}
\newlabel{text/keywords:key-mpole-taper}{{8.3}{84}{Description of Individual Keywords}{section*.249}{}}
\newlabel{text/keywords:key-multipole}{{8.3}{84}{Description of Individual Keywords}{section*.250}{}}
\newlabel{text/keywords:key-multipoleterm}{{8.3}{85}{Description of Individual Keywords}{section*.251}{}}
\newlabel{text/keywords:key-mutate}{{8.3}{85}{Description of Individual Keywords}{section*.252}{}}
\newlabel{text/keywords:key-mutual-11-scale}{{8.3}{85}{Description of Individual Keywords}{section*.253}{}}
\newlabel{text/keywords:key-mutual-12-scale}{{8.3}{85}{Description of Individual Keywords}{section*.254}{}}
\newlabel{text/keywords:key-mutual-13-scale}{{8.3}{85}{Description of Individual Keywords}{section*.255}{}}
\newlabel{text/keywords:key-mutual-14-scale}{{8.3}{85}{Description of Individual Keywords}{section*.256}{}}
\newlabel{text/keywords:key-neck-correction}{{8.3}{85}{Description of Individual Keywords}{section*.257}{}}
\newlabel{text/keywords:key-neighbor-groups}{{8.3}{85}{Description of Individual Keywords}{section*.258}{}}
\newlabel{text/keywords:key-neighbor-list}{{8.3}{86}{Description of Individual Keywords}{section*.259}{}}
\newlabel{text/keywords:key-neutral-groups}{{8.3}{86}{Description of Individual Keywords}{section*.260}{}}
\newlabel{text/keywords:key-newhess}{{8.3}{86}{Description of Individual Keywords}{section*.261}{}}
\newlabel{text/keywords:key-nextiter}{{8.3}{86}{Description of Individual Keywords}{section*.262}{}}
\newlabel{text/keywords:key-noarchive}{{8.3}{86}{Description of Individual Keywords}{section*.263}{}}
\newlabel{text/keywords:key-nonbondterm}{{8.3}{86}{Description of Individual Keywords}{section*.264}{}}
\newlabel{text/keywords:key-nodescreen}{{8.3}{86}{Description of Individual Keywords}{section*.265}{}}
\newlabel{text/keywords:key-nosymmetry}{{8.3}{86}{Description of Individual Keywords}{section*.266}{}}
\newlabel{text/keywords:key-noversion}{{8.3}{86}{Description of Individual Keywords}{section*.267}{}}
\newlabel{text/keywords:key-octahedron}{{8.3}{87}{Description of Individual Keywords}{section*.268}{}}
\newlabel{text/keywords:key-onion-probe}{{8.3}{87}{Description of Individual Keywords}{section*.269}{}}
\newlabel{text/keywords:key-opbend}{{8.3}{87}{Description of Individual Keywords}{section*.270}{}}
\newlabel{text/keywords:key-opbend-cubic}{{8.3}{87}{Description of Individual Keywords}{section*.271}{}}
\newlabel{text/keywords:key-opbend-pentic}{{8.3}{87}{Description of Individual Keywords}{section*.272}{}}
\newlabel{text/keywords:key-opbend-quartic}{{8.3}{87}{Description of Individual Keywords}{section*.273}{}}
\newlabel{text/keywords:key-opbend-sextic}{{8.3}{87}{Description of Individual Keywords}{section*.274}{}}
\newlabel{text/keywords:key-opbendterm}{{8.3}{88}{Description of Individual Keywords}{section*.275}{}}
\newlabel{text/keywords:key-opbendtype}{{8.3}{88}{Description of Individual Keywords}{section*.276}{}}
\newlabel{text/keywords:key-opbendunit}{{8.3}{88}{Description of Individual Keywords}{section*.277}{}}
\newlabel{text/keywords:key-opdist}{{8.3}{88}{Description of Individual Keywords}{section*.278}{}}
\newlabel{text/keywords:key-opdist-cubic}{{8.3}{88}{Description of Individual Keywords}{section*.279}{}}
\newlabel{text/keywords:key-opdist-pentic}{{8.3}{88}{Description of Individual Keywords}{section*.280}{}}
\newlabel{text/keywords:key-opdist-quartic}{{8.3}{89}{Description of Individual Keywords}{section*.281}{}}
\newlabel{text/keywords:key-opdist-sextic}{{8.3}{89}{Description of Individual Keywords}{section*.282}{}}
\newlabel{text/keywords:key-opdistterm}{{8.3}{89}{Description of Individual Keywords}{section*.283}{}}
\newlabel{text/keywords:key-opdistunit}{{8.3}{89}{Description of Individual Keywords}{section*.284}{}}
\newlabel{text/keywords:key-openmp-threads}{{8.3}{89}{Description of Individual Keywords}{section*.285}{}}
\newlabel{text/keywords:key-opt-coeff}{{8.3}{89}{Description of Individual Keywords}{section*.286}{}}
\newlabel{text/keywords:key-overwrite}{{8.3}{89}{Description of Individual Keywords}{section*.287}{}}
\newlabel{text/keywords:key-parameters}{{8.3}{89}{Description of Individual Keywords}{section*.288}{}}
\newlabel{text/keywords:key-pbtype}{{8.3}{90}{Description of Individual Keywords}{section*.289}{}}
\newlabel{text/keywords:key-pcg-guess}{{8.3}{90}{Description of Individual Keywords}{section*.290}{}}
\newlabel{text/keywords:key-pcg-noguess}{{8.3}{90}{Description of Individual Keywords}{section*.291}{}}
\newlabel{text/keywords:key-pcg-noprecond}{{8.3}{90}{Description of Individual Keywords}{section*.292}{}}
\newlabel{text/keywords:key-pcg-peek}{{8.3}{90}{Description of Individual Keywords}{section*.293}{}}
\newlabel{text/keywords:key-pcg-precond}{{8.3}{90}{Description of Individual Keywords}{section*.294}{}}
\newlabel{text/keywords:key-penetration}{{8.3}{90}{Description of Individual Keywords}{section*.295}{}}
\newlabel{text/keywords:key-pewald-alpha}{{8.3}{90}{Description of Individual Keywords}{section*.296}{}}
\newlabel{text/keywords:key-piatom}{{8.3}{90}{Description of Individual Keywords}{section*.297}{}}
\newlabel{text/keywords:key-pibond}{{8.3}{90}{Description of Individual Keywords}{section*.298}{}}
\newlabel{text/keywords:key-pibond4}{{8.3}{90}{Description of Individual Keywords}{section*.299}{}}
\newlabel{text/keywords:key-pibond5}{{8.3}{90}{Description of Individual Keywords}{section*.300}{}}
\newlabel{text/keywords:key-pisystem}{{8.3}{90}{Description of Individual Keywords}{section*.301}{}}
\newlabel{text/keywords:key-pitors}{{8.3}{91}{Description of Individual Keywords}{section*.302}{}}
\newlabel{text/keywords:key-pitorsterm}{{8.3}{91}{Description of Individual Keywords}{section*.303}{}}
\newlabel{text/keywords:key-pitorsunit}{{8.3}{91}{Description of Individual Keywords}{section*.304}{}}
\newlabel{text/keywords:key-pme-grid}{{8.3}{91}{Description of Individual Keywords}{section*.305}{}}
\newlabel{text/keywords:key-pme-order}{{8.3}{91}{Description of Individual Keywords}{section*.306}{}}
\newlabel{text/keywords:key-polar-12-intra}{{8.3}{91}{Description of Individual Keywords}{section*.307}{}}
\newlabel{text/keywords:key-polar-12-scale}{{8.3}{91}{Description of Individual Keywords}{section*.308}{}}
\newlabel{text/keywords:key-polar-13-intra}{{8.3}{91}{Description of Individual Keywords}{section*.309}{}}
\newlabel{text/keywords:key-polar-13-scale}{{8.3}{91}{Description of Individual Keywords}{section*.310}{}}
\newlabel{text/keywords:key-polar-14-intra}{{8.3}{92}{Description of Individual Keywords}{section*.311}{}}
\newlabel{text/keywords:key-polar-14-scale}{{8.3}{92}{Description of Individual Keywords}{section*.312}{}}
\newlabel{text/keywords:key-polar-15-intra}{{8.3}{92}{Description of Individual Keywords}{section*.313}{}}
\newlabel{text/keywords:key-polar-15-scale}{{8.3}{92}{Description of Individual Keywords}{section*.314}{}}
\newlabel{text/keywords:key-polar-eps}{{8.3}{92}{Description of Individual Keywords}{section*.315}{}}
\newlabel{text/keywords:key-polar-iter}{{8.3}{92}{Description of Individual Keywords}{section*.316}{}}
\newlabel{text/keywords:key-polar-predict}{{8.3}{92}{Description of Individual Keywords}{section*.317}{}}
\newlabel{text/keywords:key-polarizable}{{8.3}{92}{Description of Individual Keywords}{section*.318}{}}
\newlabel{text/keywords:key-polarization}{{8.3}{92}{Description of Individual Keywords}{section*.319}{}}
\newlabel{text/keywords:key-polarize}{{8.3}{93}{Description of Individual Keywords}{section*.320}{}}
\newlabel{text/keywords:key-polarizeterm}{{8.3}{93}{Description of Individual Keywords}{section*.321}{}}
\newlabel{text/keywords:key-polpair}{{8.3}{93}{Description of Individual Keywords}{section*.322}{}}
\newlabel{text/keywords:key-polymer-cutoff}{{8.3}{93}{Description of Individual Keywords}{section*.323}{}}
\newlabel{text/keywords:key-potential-atoms}{{8.3}{93}{Description of Individual Keywords}{section*.324}{}}
\newlabel{text/keywords:key-potential-factor}{{8.3}{93}{Description of Individual Keywords}{section*.325}{}}
\newlabel{text/keywords:key-potential-fit}{{8.3}{93}{Description of Individual Keywords}{section*.326}{}}
\newlabel{text/keywords:key-potential-offset}{{8.3}{94}{Description of Individual Keywords}{section*.327}{}}
\newlabel{text/keywords:key-potential-shells}{{8.3}{94}{Description of Individual Keywords}{section*.328}{}}
\newlabel{text/keywords:key-potential-spacing}{{8.3}{94}{Description of Individual Keywords}{section*.329}{}}
\newlabel{text/keywords:key-ppme-order}{{8.3}{94}{Description of Individual Keywords}{section*.330}{}}
\newlabel{text/keywords:key-pressure}{{8.3}{94}{Description of Individual Keywords}{section*.331}{}}
\newlabel{text/keywords:key-printout}{{8.3}{94}{Description of Individual Keywords}{section*.332}{}}
\newlabel{text/keywords:key-radiusrule}{{8.3}{94}{Description of Individual Keywords}{section*.333}{}}
\newlabel{text/keywords:key-radiussize}{{8.3}{94}{Description of Individual Keywords}{section*.334}{}}
\newlabel{text/keywords:key-radiustype}{{8.3}{94}{Description of Individual Keywords}{section*.335}{}}
\newlabel{text/keywords:key-randomseed}{{8.3}{95}{Description of Individual Keywords}{section*.336}{}}
\newlabel{text/keywords:key-reduce}{{8.3}{95}{Description of Individual Keywords}{section*.337}{}}
\newlabel{text/keywords:key-remove-inertia}{{8.3}{95}{Description of Individual Keywords}{section*.338}{}}
\newlabel{text/keywords:key-rep-12-scale}{{8.3}{95}{Description of Individual Keywords}{section*.339}{}}
\newlabel{text/keywords:key-rep-13-scale}{{8.3}{95}{Description of Individual Keywords}{section*.340}{}}
\newlabel{text/keywords:key-rep-14-scale}{{8.3}{95}{Description of Individual Keywords}{section*.341}{}}
\newlabel{text/keywords:key-rep-15-scale}{{8.3}{95}{Description of Individual Keywords}{section*.342}{}}
\newlabel{text/keywords:key-repuls-cutoff}{{8.3}{96}{Description of Individual Keywords}{section*.343}{}}
\newlabel{text/keywords:key-repuls-taper}{{8.3}{96}{Description of Individual Keywords}{section*.344}{}}
\newlabel{text/keywords:key-repulsion}{{8.3}{96}{Description of Individual Keywords}{section*.345}{}}
\newlabel{text/keywords:key-repulsionterm}{{8.3}{96}{Description of Individual Keywords}{section*.346}{}}
\newlabel{text/keywords:key-resp-weight}{{8.3}{96}{Description of Individual Keywords}{section*.347}{}}
\newlabel{text/keywords:key-respa-inner}{{8.3}{96}{Description of Individual Keywords}{section*.348}{}}
\newlabel{text/keywords:key-resptype}{{8.3}{96}{Description of Individual Keywords}{section*.349}{}}
\newlabel{text/keywords:key-restrain-angle}{{8.3}{96}{Description of Individual Keywords}{section*.350}{}}
\newlabel{text/keywords:key-restrain-distance}{{8.3}{97}{Description of Individual Keywords}{section*.351}{}}
\newlabel{text/keywords:key-restrain-groups}{{8.3}{97}{Description of Individual Keywords}{section*.352}{}}
\newlabel{text/keywords:key-restrain-plane}{{8.3}{97}{Description of Individual Keywords}{section*.353}{}}
\newlabel{text/keywords:key-restrain-position}{{8.3}{97}{Description of Individual Keywords}{section*.354}{}}
\newlabel{text/keywords:key-restrain-torsion}{{8.3}{98}{Description of Individual Keywords}{section*.355}{}}
\newlabel{text/keywords:key-restrainterm}{{8.3}{98}{Description of Individual Keywords}{section*.356}{}}
\newlabel{text/keywords:key-rotatable-bond}{{8.3}{98}{Description of Individual Keywords}{section*.357}{}}
\newlabel{text/keywords:key-rxnfieldterm}{{8.3}{98}{Description of Individual Keywords}{section*.358}{}}
\newlabel{text/keywords:key-saddlepoint}{{8.3}{98}{Description of Individual Keywords}{section*.359}{}}
\newlabel{text/keywords:key-save-cycle}{{8.3}{98}{Description of Individual Keywords}{section*.360}{}}
\newlabel{text/keywords:key-save-force}{{8.3}{98}{Description of Individual Keywords}{section*.361}{}}
\newlabel{text/keywords:key-save-induced}{{8.3}{98}{Description of Individual Keywords}{section*.362}{}}
\newlabel{text/keywords:key-save-vects}{{8.3}{98}{Description of Individual Keywords}{section*.363}{}}
\newlabel{text/keywords:key-save-velocity}{{8.3}{99}{Description of Individual Keywords}{section*.364}{}}
\newlabel{text/keywords:key-slopemax}{{8.3}{99}{Description of Individual Keywords}{section*.365}{}}
\newlabel{text/keywords:key-smoothing}{{8.3}{99}{Description of Individual Keywords}{section*.366}{}}
\newlabel{text/keywords:key-solute}{{8.3}{99}{Description of Individual Keywords}{section*.367}{}}
\newlabel{text/keywords:key-solvate}{{8.3}{99}{Description of Individual Keywords}{section*.368}{}}
\newlabel{text/keywords:key-solvateterm}{{8.3}{99}{Description of Individual Keywords}{section*.369}{}}
\newlabel{text/keywords:key-solvent-pressure}{{8.3}{99}{Description of Individual Keywords}{section*.370}{}}
\newlabel{text/keywords:key-spacegroup}{{8.3}{99}{Description of Individual Keywords}{section*.371}{}}
\newlabel{text/keywords:key-steepest-descent}{{8.3}{100}{Description of Individual Keywords}{section*.372}{}}
\newlabel{text/keywords:key-stepmax}{{8.3}{100}{Description of Individual Keywords}{section*.373}{}}
\newlabel{text/keywords:key-stepmin}{{8.3}{100}{Description of Individual Keywords}{section*.374}{}}
\newlabel{text/keywords:key-strbnd}{{8.3}{100}{Description of Individual Keywords}{section*.375}{}}
\newlabel{text/keywords:key-strbndterm}{{8.3}{100}{Description of Individual Keywords}{section*.376}{}}
\newlabel{text/keywords:key-strbndunit}{{8.3}{100}{Description of Individual Keywords}{section*.377}{}}
\newlabel{text/keywords:key-strtors}{{8.3}{100}{Description of Individual Keywords}{section*.378}{}}
\newlabel{text/keywords:key-strtorterm}{{8.3}{101}{Description of Individual Keywords}{section*.379}{}}
\newlabel{text/keywords:key-strtorunit}{{8.3}{101}{Description of Individual Keywords}{section*.380}{}}
\newlabel{text/keywords:key-surface-tension}{{8.3}{101}{Description of Individual Keywords}{section*.381}{}}
\newlabel{text/keywords:key-tanh-correction}{{8.3}{101}{Description of Individual Keywords}{section*.382}{}}
\newlabel{text/keywords:key-taper}{{8.3}{101}{Description of Individual Keywords}{section*.383}{}}
\newlabel{text/keywords:key-target-dipole}{{8.3}{101}{Description of Individual Keywords}{section*.384}{}}
\newlabel{text/keywords:key-target-quadrupole}{{8.3}{101}{Description of Individual Keywords}{section*.385}{}}
\newlabel{text/keywords:key-tau-pressure}{{8.3}{101}{Description of Individual Keywords}{section*.386}{}}
\newlabel{text/keywords:key-tau-temperature}{{8.3}{101}{Description of Individual Keywords}{section*.387}{}}
\newlabel{text/keywords:key-tcg-guess}{{8.3}{101}{Description of Individual Keywords}{section*.388}{}}
\newlabel{text/keywords:key-tcg-noguess}{{8.3}{101}{Description of Individual Keywords}{section*.389}{}}
\newlabel{text/keywords:key-tcg-peek}{{8.3}{101}{Description of Individual Keywords}{section*.390}{}}
\newlabel{text/keywords:key-thermostat}{{8.3}{101}{Description of Individual Keywords}{section*.391}{}}
\newlabel{text/keywords:key-tors-lambda}{{8.3}{102}{Description of Individual Keywords}{section*.392}{}}
\newlabel{text/keywords:key-torsion}{{8.3}{102}{Description of Individual Keywords}{section*.393}{}}
\newlabel{text/keywords:key-torsion4}{{8.3}{102}{Description of Individual Keywords}{section*.394}{}}
\newlabel{text/keywords:key-torsion5}{{8.3}{102}{Description of Individual Keywords}{section*.395}{}}
\newlabel{text/keywords:key-torsionterm}{{8.3}{102}{Description of Individual Keywords}{section*.396}{}}
\newlabel{text/keywords:key-torsionunit}{{8.3}{102}{Description of Individual Keywords}{section*.397}{}}
\newlabel{text/keywords:key-tortors}{{8.3}{102}{Description of Individual Keywords}{section*.398}{}}
\newlabel{text/keywords:key-tortorterm}{{8.3}{103}{Description of Individual Keywords}{section*.399}{}}
\newlabel{text/keywords:key-tortorunit}{{8.3}{103}{Description of Individual Keywords}{section*.400}{}}
\newlabel{text/keywords:key-trial-distance}{{8.3}{103}{Description of Individual Keywords}{section*.401}{}}
\newlabel{text/keywords:key-trial-distribution}{{8.3}{103}{Description of Individual Keywords}{section*.402}{}}
\newlabel{text/keywords:key-truncate}{{8.3}{103}{Description of Individual Keywords}{section*.403}{}}
\newlabel{text/keywords:unwrap-coords}{{8.3}{103}{Description of Individual Keywords}{section*.404}{}}
\newlabel{text/keywords:key-urey-cubic}{{8.3}{103}{Description of Individual Keywords}{section*.405}{}}
\newlabel{text/keywords:key-urey-quartic}{{8.3}{103}{Description of Individual Keywords}{section*.406}{}}
\newlabel{text/keywords:key-ureybrad}{{8.3}{104}{Description of Individual Keywords}{section*.407}{}}
\newlabel{text/keywords:key-ureyterm}{{8.3}{104}{Description of Individual Keywords}{section*.408}{}}
\newlabel{text/keywords:key-ureyunit}{{8.3}{104}{Description of Individual Keywords}{section*.409}{}}
\newlabel{text/keywords:key-usolve-accel}{{8.3}{104}{Description of Individual Keywords}{section*.410}{}}
\newlabel{text/keywords:key-usolve-buffer}{{8.3}{104}{Description of Individual Keywords}{section*.411}{}}
\newlabel{text/keywords:key-usolve-cutoff}{{8.3}{104}{Description of Individual Keywords}{section*.412}{}}
\newlabel{text/keywords:key-usolve-diagonal}{{8.3}{104}{Description of Individual Keywords}{section*.413}{}}
\newlabel{text/keywords:key-usolve-list}{{8.3}{104}{Description of Individual Keywords}{section*.414}{}}
\newlabel{text/keywords:key-valenceterm}{{8.3}{104}{Description of Individual Keywords}{section*.415}{}}
\newlabel{text/keywords:key-vdw}{{8.3}{105}{Description of Individual Keywords}{section*.416}{}}
\newlabel{text/keywords:key-vdw-12-scale}{{8.3}{105}{Description of Individual Keywords}{section*.417}{}}
\newlabel{text/keywords:key-vdw-13-scale}{{8.3}{105}{Description of Individual Keywords}{section*.418}{}}
\newlabel{text/keywords:key-vdw-14-scale}{{8.3}{105}{Description of Individual Keywords}{section*.419}{}}
\newlabel{text/keywords:key-vdw-15-scale}{{8.3}{105}{Description of Individual Keywords}{section*.420}{}}
\newlabel{text/keywords:key-vdw-annihilate}{{8.3}{105}{Description of Individual Keywords}{section*.421}{}}
\newlabel{text/keywords:key-vdw-correction}{{8.3}{105}{Description of Individual Keywords}{section*.422}{}}
\newlabel{text/keywords:key-vdw-cutoff}{{8.3}{105}{Description of Individual Keywords}{section*.423}{}}
\newlabel{text/keywords:key-vdw-lambda}{{8.3}{106}{Description of Individual Keywords}{section*.424}{}}
\newlabel{text/keywords:key-vdw-list}{{8.3}{106}{Description of Individual Keywords}{section*.425}{}}
\newlabel{text/keywords:key-vdw-taper}{{8.3}{106}{Description of Individual Keywords}{section*.426}{}}
\newlabel{text/keywords:key-vdw14}{{8.3}{106}{Description of Individual Keywords}{section*.427}{}}
\newlabel{text/keywords:key-vdwindex}{{8.3}{106}{Description of Individual Keywords}{section*.428}{}}
\newlabel{text/keywords:key-vdwpair}{{8.3}{106}{Description of Individual Keywords}{section*.429}{}}
\newlabel{text/keywords:key-vdwterm}{{8.3}{106}{Description of Individual Keywords}{section*.430}{}}
\newlabel{text/keywords:key-vdwtype}{{8.3}{106}{Description of Individual Keywords}{section*.431}{}}
\newlabel{text/keywords:key-verbose}{{8.3}{107}{Description of Individual Keywords}{section*.432}{}}
\newlabel{text/keywords:key-vib-roots}{{8.3}{107}{Description of Individual Keywords}{section*.433}{}}
\newlabel{text/keywords:key-vib-tolerance}{{8.3}{107}{Description of Individual Keywords}{section*.434}{}}
\newlabel{text/keywords:key-volume-move}{{8.3}{107}{Description of Individual Keywords}{section*.435}{}}
\newlabel{text/keywords:key-volume-scale}{{8.3}{107}{Description of Individual Keywords}{section*.436}{}}
\newlabel{text/keywords:key-volume-trial}{{8.3}{107}{Description of Individual Keywords}{section*.437}{}}
\newlabel{text/keywords:key-wall}{{8.3}{107}{Description of Individual Keywords}{section*.438}{}}
\newlabel{text/keywords:wrap-coords}{{8.3}{107}{Description of Individual Keywords}{section*.439}{}}
\newlabel{text/keywords:key-writeout}{{8.3}{107}{Description of Individual Keywords}{section*.440}{}}
\newlabel{text/keywords:key-x-axis}{{8.3}{107}{Description of Individual Keywords}{section*.441}{}}
\newlabel{text/keywords:key-y-axis}{{8.3}{108}{Description of Individual Keywords}{section*.442}{}}
\newlabel{text/keywords:key-z-axis}{{8.3}{108}{Description of Individual Keywords}{section*.443}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {9}Routines \& Functions}{109}{chapter.9}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/routines:routines-functions}{{9}{109}{Routines \& Functions}{chapter.9}{}}
\newlabel{text/routines::doc}{{9}{109}{Routines \& Functions}{chapter.9}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {10}Modules \& Global Variables}{203}{chapter.10}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/modules:modules-global-variables}{{10}{203}{Modules \& Global Variables}{chapter.10}{}}
\newlabel{text/modules::doc}{{10}{203}{Modules \& Global Variables}{chapter.10}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {11}Test Cases \& Examples}{251}{chapter.11}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/test-cases:test-cases-examples}{{11}{251}{Test Cases \& Examples}{chapter.11}{}}
\newlabel{text/test-cases::doc}{{11}{251}{Test Cases \& Examples}{chapter.11}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {12}Benchmark Results}{255}{chapter.12}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/benchmarks:benchmark-results}{{12}{255}{Benchmark Results}{chapter.12}{}}
\newlabel{text/benchmarks::doc}{{12}{255}{Benchmark Results}{chapter.12}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.1}Calmodulin Energy Evaluation (Serial)}{255}{section.12.1}\protected@file@percent }
\newlabel{text/benchmarks:calmodulin-energy-evaluation-serial}{{12.1}{255}{Calmodulin Energy Evaluation (Serial)}{section.12.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.2}Crambin Crystal Energy Evaluation (Serial)}{255}{section.12.2}\protected@file@percent }
\newlabel{text/benchmarks:crambin-crystal-energy-evaluation-serial}{{12.2}{255}{Crambin Crystal Energy Evaluation (Serial)}{section.12.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.3}Crambin Normal Mode Calculation (Serial)}{256}{section.12.3}\protected@file@percent }
\newlabel{text/benchmarks:crambin-normal-mode-calculation-serial}{{12.3}{256}{Crambin Normal Mode Calculation (Serial)}{section.12.3}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.4}Water Box Molecular Dynamics using TIP3P (Serial)}{256}{section.12.4}\protected@file@percent }
\newlabel{text/benchmarks:water-box-molecular-dynamics-using-tip3p-serial}{{12.4}{256}{Water Box Molecular Dynamics using TIP3P (Serial)}{section.12.4}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.5}Water Box Molecular Dynamics using AMOEBA (Serial)}{256}{section.12.5}\protected@file@percent }
\newlabel{text/benchmarks:water-box-molecular-dynamics-using-amoeba-serial}{{12.5}{256}{Water Box Molecular Dynamics using AMOEBA (Serial)}{section.12.5}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.6}MD on DHFR in Water using CHARMM (OpenMP Parallel)}{256}{section.12.6}\protected@file@percent }
\newlabel{text/benchmarks:md-on-dhfr-in-water-using-charmm-openmp-parallel}{{12.6}{256}{MD on DHFR in Water using CHARMM (OpenMP Parallel)}{section.12.6}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.7}MD on DHFR in Water using AMOEBA (OpenMP Parallel)}{257}{section.12.7}\protected@file@percent }
\newlabel{text/benchmarks:md-on-dhfr-in-water-using-amoeba-openmp-parallel}{{12.7}{257}{MD on DHFR in Water using AMOEBA (OpenMP Parallel)}{section.12.7}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.8}MD on COX\sphinxhyphen {}2 in Water using OPLS\sphinxhyphen {}AA (OpenMP Parallel)}{258}{section.12.8}\protected@file@percent }
\newlabel{text/benchmarks:md-on-cox-2-in-water-using-opls-aa-openmp-parallel}{{12.8}{258}{MD on COX\sphinxhyphen {}2 in Water using OPLS\sphinxhyphen {}AA (OpenMP Parallel)}{section.12.8}{}}
\@writefile{toc}{\contentsline {section}{\numberline {12.9}MD on COX\sphinxhyphen {}2 in Water using AMOEBA (OpenMP Parallel)}{258}{section.12.9}\protected@file@percent }
\newlabel{text/benchmarks:md-on-cox-2-in-water-using-amoeba-openmp-parallel}{{12.9}{258}{MD on COX\sphinxhyphen {}2 in Water using AMOEBA (OpenMP Parallel)}{section.12.9}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {13}Acknowledgments}{261}{chapter.13}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/acknowledgements:acknowledgments}{{13}{261}{Acknowledgments}{chapter.13}{}}
\newlabel{text/acknowledgements::doc}{{13}{261}{Acknowledgments}{chapter.13}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {14}References}{265}{chapter.14}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{text/references:references}{{14}{265}{References}{chapter.14}{}}
\newlabel{text/references::doc}{{14}{265}{References}{chapter.14}{}}
\@writefile{toc}{\contentsline {section}{\numberline {14.1}Molecular Mechanics \& Dynamics Software Packages}{265}{section.14.1}\protected@file@percent }
\newlabel{text/references:molecular-mechanics-dynamics-software-packages}{{14.1}{265}{Molecular Mechanics \& Dynamics Software Packages}{section.14.1}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.1.1}Tinker Software Tools}{265}{subsection.14.1.1}\protected@file@percent }
\newlabel{text/references:tinker-software-tools}{{14.1.1}{265}{Tinker Software Tools}{subsection.14.1.1}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.1.2}Alternative Molecular Modeling Software}{266}{subsection.14.1.2}\protected@file@percent }
\newlabel{text/references:alternative-molecular-modeling-software}{{14.1.2}{266}{Alternative Molecular Modeling Software}{subsection.14.1.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {14.2}Literature References by Topic}{271}{section.14.2}\protected@file@percent }
\newlabel{text/references:literature-references-by-topic}{{14.2}{271}{Literature References by Topic}{section.14.2}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.1}Molecular Mechanics Methodology}{271}{subsection.14.2.1}\protected@file@percent }
\newlabel{text/references:molecular-mechanics-methodology}{{14.2.1}{271}{Molecular Mechanics Methodology}{subsection.14.2.1}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.2}Intermolecular Interactions}{271}{subsection.14.2.2}\protected@file@percent }
\newlabel{text/references:intermolecular-interactions}{{14.2.2}{271}{Intermolecular Interactions}{subsection.14.2.2}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.3}Computer Simulation Methodology}{271}{subsection.14.2.3}\protected@file@percent }
\newlabel{text/references:computer-simulation-methodology}{{14.2.3}{271}{Computer Simulation Methodology}{subsection.14.2.3}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.4}Modeling of Biological Macromolecules}{272}{subsection.14.2.4}\protected@file@percent }
\newlabel{text/references:modeling-of-biological-macromolecules}{{14.2.4}{272}{Modeling of Biological Macromolecules}{subsection.14.2.4}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.5}Nonlinear Optimization Algorithms}{272}{subsection.14.2.5}\protected@file@percent }
\newlabel{text/references:nonlinear-optimization-algorithms}{{14.2.5}{272}{Nonlinear Optimization Algorithms}{subsection.14.2.5}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.6}Truncated Newton Optimization}{273}{subsection.14.2.6}\protected@file@percent }
\newlabel{text/references:truncated-newton-optimization}{{14.2.6}{273}{Truncated Newton Optimization}{subsection.14.2.6}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.7}Potential Energy Smoothing}{273}{subsection.14.2.7}\protected@file@percent }
\newlabel{text/references:potential-energy-smoothing}{{14.2.7}{273}{Potential Energy Smoothing}{subsection.14.2.7}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.8}“Sniffer” Global Optimization}{274}{subsection.14.2.8}\protected@file@percent }
\newlabel{text/references:sniffer-global-optimization}{{14.2.8}{274}{“Sniffer” Global Optimization}{subsection.14.2.8}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.9}Integration Methods for Molecular Dynamics}{274}{subsection.14.2.9}\protected@file@percent }
\newlabel{text/references:integration-methods-for-molecular-dynamics}{{14.2.9}{274}{Integration Methods for Molecular Dynamics}{subsection.14.2.9}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.10}Constraint Dynamics}{275}{subsection.14.2.10}\protected@file@percent }
\newlabel{text/references:constraint-dynamics}{{14.2.10}{275}{Constraint Dynamics}{subsection.14.2.10}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.11}Langevin, Brownian and Stochastic Dynamics}{275}{subsection.14.2.11}\protected@file@percent }
\newlabel{text/references:langevin-brownian-and-stochastic-dynamics}{{14.2.11}{275}{Langevin, Brownian and Stochastic Dynamics}{subsection.14.2.11}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.12}Constant Temperature and Pressure Dynamics}{275}{subsection.14.2.12}\protected@file@percent }
\newlabel{text/references:constant-temperature-and-pressure-dynamics}{{14.2.12}{275}{Constant Temperature and Pressure Dynamics}{subsection.14.2.12}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.13}Out\sphinxhyphen {}of\sphinxhyphen {}Plane Deformation Terms}{276}{subsection.14.2.13}\protected@file@percent }
\newlabel{text/references:out-of-plane-deformation-terms}{{14.2.13}{276}{Out\sphinxhyphen {}of\sphinxhyphen {}Plane Deformation Terms}{subsection.14.2.13}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.14}Geometry\sphinxhyphen {}Dependent Charge Flux Terms}{276}{subsection.14.2.14}\protected@file@percent }
\newlabel{text/references:geometry-dependent-charge-flux-terms}{{14.2.14}{276}{Geometry\sphinxhyphen {}Dependent Charge Flux Terms}{subsection.14.2.14}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.15}Analytical Derivatives of Potential Functions}{276}{subsection.14.2.15}\protected@file@percent }
\newlabel{text/references:analytical-derivatives-of-potential-functions}{{14.2.15}{276}{Analytical Derivatives of Potential Functions}{subsection.14.2.15}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.16}Torsional Space Derivatives and Normal Modes}{277}{subsection.14.2.16}\protected@file@percent }
\newlabel{text/references:torsional-space-derivatives-and-normal-modes}{{14.2.16}{277}{Torsional Space Derivatives and Normal Modes}{subsection.14.2.16}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.17}Analytical Surface Area and Volume}{277}{subsection.14.2.17}\protected@file@percent }
\newlabel{text/references:analytical-surface-area-and-volume}{{14.2.17}{277}{Analytical Surface Area and Volume}{subsection.14.2.17}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.18}Approximate Surface Area and Volume}{278}{subsection.14.2.18}\protected@file@percent }
\newlabel{text/references:approximate-surface-area-and-volume}{{14.2.18}{278}{Approximate Surface Area and Volume}{subsection.14.2.18}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.19}Boundary Conditions and Neighbor Methods}{278}{subsection.14.2.19}\protected@file@percent }
\newlabel{text/references:boundary-conditions-and-neighbor-methods}{{14.2.19}{278}{Boundary Conditions and Neighbor Methods}{subsection.14.2.19}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.20}Cutoff and Truncation Methods}{278}{subsection.14.2.20}\protected@file@percent }
\newlabel{text/references:cutoff-and-truncation-methods}{{14.2.20}{278}{Cutoff and Truncation Methods}{subsection.14.2.20}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.21}Ewald Summation Techniques}{279}{subsection.14.2.21}\protected@file@percent }
\newlabel{text/references:ewald-summation-techniques}{{14.2.21}{279}{Ewald Summation Techniques}{subsection.14.2.21}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.22}Conjugated and Aromatic Systems}{279}{subsection.14.2.22}\protected@file@percent }
\newlabel{text/references:conjugated-and-aromatic-systems}{{14.2.22}{279}{Conjugated and Aromatic Systems}{subsection.14.2.22}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.23}Free Energy Simulation Methods}{280}{subsection.14.2.23}\protected@file@percent }
\newlabel{text/references:free-energy-simulation-methods}{{14.2.23}{280}{Free Energy Simulation Methods}{subsection.14.2.23}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.24}Methods for Parameter Determination}{280}{subsection.14.2.24}\protected@file@percent }
\newlabel{text/references:methods-for-parameter-determination}{{14.2.24}{280}{Methods for Parameter Determination}{subsection.14.2.24}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.25}Electrostatic Interactions}{281}{subsection.14.2.25}\protected@file@percent }
\newlabel{text/references:electrostatic-interactions}{{14.2.25}{281}{Electrostatic Interactions}{subsection.14.2.25}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.26}Polarization Effects}{281}{subsection.14.2.26}\protected@file@percent }
\newlabel{text/references:polarization-effects}{{14.2.26}{281}{Polarization Effects}{subsection.14.2.26}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.27}Macroscopic Treatment of Solvent}{282}{subsection.14.2.27}\protected@file@percent }
\newlabel{text/references:macroscopic-treatment-of-solvent}{{14.2.27}{282}{Macroscopic Treatment of Solvent}{subsection.14.2.27}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.28}Surface Area\sphinxhyphen {}Based Solvation Models}{282}{subsection.14.2.28}\protected@file@percent }
\newlabel{text/references:surface-area-based-solvation-models}{{14.2.28}{282}{Surface Area\sphinxhyphen {}Based Solvation Models}{subsection.14.2.28}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.29}Generalized Born Solvation Models}{282}{subsection.14.2.29}\protected@file@percent }
\newlabel{text/references:generalized-born-solvation-models}{{14.2.29}{282}{Generalized Born Solvation Models}{subsection.14.2.29}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.30}Superposition of Coordinate Sets}{283}{subsection.14.2.30}\protected@file@percent }
\newlabel{text/references:superposition-of-coordinate-sets}{{14.2.30}{283}{Superposition of Coordinate Sets}{subsection.14.2.30}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {14.2.31}Location of Transition States}{283}{subsection.14.2.31}\protected@file@percent }
\newlabel{text/references:location-of-transition-states}{{14.2.31}{283}{Location of Transition States}{subsection.14.2.31}{}}
\@writefile{toc}{\contentsline {chapter}{Index}{285}{section*.444}\protected@file@percent }
\gdef \@abspage@last{294}
