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mw-list-item"><a href="https://ca.wikipedia.org/wiki/Simulaci%C3%B3_molecular" title="Simulació molecular – Catalan" lang="ca" hreflang="ca" data-title="Simulació molecular" data-language-autonym="Català" data-language-local-name="Catalan" class="interlanguage-link-target"><span>Català</span></a></li><li class="interlanguage-link interwiki-cs mw-list-item"><a href="https://cs.wikipedia.org/wiki/Molekul%C3%A1rn%C3%AD_modelov%C3%A1n%C3%AD" title="Molekulární modelování – Czech" lang="cs" hreflang="cs" data-title="Molekulární modelování" data-language-autonym="Čeština" data-language-local-name="Czech" class="interlanguage-link-target"><span>Čeština</span></a></li><li class="interlanguage-link interwiki-de mw-list-item"><a href="https://de.wikipedia.org/wiki/Molekulare_Modellierung" title="Molekulare Modellierung – German" lang="de" hreflang="de" data-title="Molekulare Modellierung" data-language-autonym="Deutsch" data-language-local-name="German" class="interlanguage-link-target"><span>Deutsch</span></a></li><li class="interlanguage-link interwiki-es mw-list-item"><a href="https://es.wikipedia.org/wiki/Modelado_molecular" title="Modelado molecular – Spanish" lang="es" hreflang="es" data-title="Modelado molecular" data-language-autonym="Español" data-language-local-name="Spanish" class="interlanguage-link-target"><span>Español</span></a></li><li class="interlanguage-link interwiki-fa mw-list-item"><a href="https://fa.wikipedia.org/wiki/%D9%85%D8%AF%D9%84%E2%80%8C%D8%B3%D8%A7%D8%B2%DB%8C_%D9%85%D9%88%D9%84%DA%A9%D9%88%D9%84%DB%8C" title="مدل‌سازی مولکولی – Persian" lang="fa" hreflang="fa" data-title="مدل‌سازی مولکولی" data-language-autonym="فارسی" data-language-local-name="Persian" class="interlanguage-link-target"><span>فارسی</span></a></li><li class="interlanguage-link interwiki-fr mw-list-item"><a href="https://fr.wikipedia.org/wiki/Mod%C3%A9lisation_mol%C3%A9culaire" title="Modélisation moléculaire – French" lang="fr" hreflang="fr" data-title="Modélisation moléculaire" data-language-autonym="Français" data-language-local-name="French" class="interlanguage-link-target"><span>Français</span></a></li><li class="interlanguage-link interwiki-ko mw-list-item"><a href="https://ko.wikipedia.org/wiki/%EB%B6%84%EC%9E%90_%EB%AA%A8%EB%8D%B8%EB%A7%81" title="분자 모델링 – Korean" lang="ko" hreflang="ko" data-title="분자 모델링" data-language-autonym="한국어" data-language-local-name="Korean" class="interlanguage-link-target"><span>한국어</span></a></li><li class="interlanguage-link interwiki-it mw-list-item"><a href="https://it.wikipedia.org/wiki/Modellistica_molecolare" title="Modellistica molecolare – Italian" lang="it" hreflang="it" data-title="Modellistica molecolare" data-language-autonym="Italiano" data-language-local-name="Italian" class="interlanguage-link-target"><span>Italiano</span></a></li><li class="interlanguage-link interwiki-hu mw-list-item"><a href="https://hu.wikipedia.org/wiki/Molekulamodellez%C3%A9s" title="Molekulamodellezés – Hungarian" lang="hu" hreflang="hu" data-title="Molekulamodellezés" data-language-autonym="Magyar" data-language-local-name="Hungarian" class="interlanguage-link-target"><span>Magyar</span></a></li><li class="interlanguage-link interwiki-mn mw-list-item"><a href="https://mn.wikipedia.org/wiki/%D0%9C%D0%BE%D0%BB%D0%B5%D0%BA%D1%83%D0%BB%D1%8B%D0%BD_%D0%B7%D0%B0%D0%B3%D0%B2%D0%B0%D1%80%D1%87%D0%BB%D0%B0%D0%BB" title="Молекулын загварчлал – Mongolian" lang="mn" hreflang="mn" data-title="Молекулын загварчлал" data-language-autonym="Монгол" data-language-local-name="Mongolian" class="interlanguage-link-target"><span>Монгол</span></a></li><li class="interlanguage-link interwiki-ja mw-list-item"><a href="https://ja.wikipedia.org/wiki/%E5%88%86%E5%AD%90%E3%82%B7%E3%83%9F%E3%83%A5%E3%83%AC%E3%83%BC%E3%82%B7%E3%83%A7%E3%83%B3" title="分子シミュレーション – Japanese" lang="ja" hreflang="ja" data-title="分子シミュレーション" data-language-autonym="日本語" data-language-local-name="Japanese" class="interlanguage-link-target"><span>日本語</span></a></li><li class="interlanguage-link interwiki-pl mw-list-item"><a href="https://pl.wikipedia.org/wiki/Modelowanie_molekularne" title="Modelowanie molekularne – Polish" lang="pl" hreflang="pl" data-title="Modelowanie molekularne" data-language-autonym="Polski" data-language-local-name="Polish" class="interlanguage-link-target"><span>Polski</span></a></li><li class="interlanguage-link interwiki-pt mw-list-item"><a href="https://pt.wikipedia.org/wiki/Modelagem_molecular" title="Modelagem molecular – Portuguese" lang="pt" hreflang="pt" data-title="Modelagem molecular" data-language-autonym="Português" data-language-local-name="Portuguese" class="interlanguage-link-target"><span>Português</span></a></li><li class="interlanguage-link interwiki-ro mw-list-item"><a href="https://ro.wikipedia.org/wiki/Modelare_molecular%C4%83" title="Modelare moleculară – Romanian" lang="ro" hreflang="ro" data-title="Modelare moleculară" data-language-autonym="Română" data-language-local-name="Romanian" class="interlanguage-link-target"><span>Română</span></a></li><li class="interlanguage-link interwiki-ru mw-list-item"><a href="https://ru.wikipedia.org/wiki/%D0%9C%D0%BE%D0%BB%D0%B5%D0%BA%D1%83%D0%BB%D1%8F%D1%80%D0%BD%D0%BE%D0%B5_%D0%BC%D0%BE%D0%B4%D0%B5%D0%BB%D0%B8%D1%80%D0%BE%D0%B2%D0%B0%D0%BD%D0%B8%D0%B5" title="Молекулярное моделирование – Russian" lang="ru" hreflang="ru" data-title="Молекулярное моделирование" data-language-autonym="Русский" data-language-local-name="Russian" class="interlanguage-link-target"><span>Русский</span></a></li><li class="interlanguage-link interwiki-sk mw-list-item"><a href="https://sk.wikipedia.org/wiki/Molekulov%C3%A9_modelovanie" title="Molekulové modelovanie – Slovak" lang="sk" hreflang="sk" data-title="Molekulové modelovanie" data-language-autonym="Slovenčina" data-language-local-name="Slovak" class="interlanguage-link-target"><span>Slovenčina</span></a></li><li class="interlanguage-link interwiki-sr mw-list-item"><a href="https://sr.wikipedia.org/wiki/%D0%9C%D0%BE%D0%BB%D0%B5%D0%BA%D1%83%D0%BB%D1%81%D0%BA%D0%BE_%D0%BC%D0%BE%D0%B4%D0%B5%D0%BB%D0%B8%D1%80%D0%B0%D1%9A%D0%B5" title="Молекулско моделирање – Serbian" lang="sr" hreflang="sr" data-title="Молекулско моделирање" data-language-autonym="Српски / srpski" data-language-local-name="Serbian" class="interlanguage-link-target"><span>Српски / srpski</span></a></li><li class="interlanguage-link interwiki-sh mw-list-item"><a href="https://sh.wikipedia.org/wiki/Molekulsko_modelovanje" title="Molekulsko modelovanje – Serbo-Croatian" lang="sh" hreflang="sh" data-title="Molekulsko modelovanje" data-language-autonym="Srpskohrvatski / српскохрватски" data-language-local-name="Serbo-Croatian" class="interlanguage-link-target"><span>Srpskohrvatski / српскохрватски</span></a></li><li class="interlanguage-link interwiki-fi mw-list-item"><a href="https://fi.wikipedia.org/wiki/Molekyylimallinnus" 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</div> </div> </div> </div> </div> </nav> </div> </div> </div> <div class="vector-column-end"> <div class="vector-sticky-pinned-container"> <nav class="vector-page-tools-landmark" aria-label="Page tools"> <div id="vector-page-tools-pinned-container" class="vector-pinned-container"> </div> </nav> <nav class="vector-appearance-landmark" aria-label="Appearance"> <div id="vector-appearance-pinned-container" class="vector-pinned-container"> <div id="vector-appearance" class="vector-appearance vector-pinnable-element"> <div class="vector-pinnable-header vector-appearance-pinnable-header vector-pinnable-header-pinned" data-feature-name="appearance-pinned" data-pinnable-element-id="vector-appearance" data-pinned-container-id="vector-appearance-pinned-container" data-unpinned-container-id="vector-appearance-unpinned-container" > <div class="vector-pinnable-header-label">Appearance</div> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-pin-button" data-event-name="pinnable-header.vector-appearance.pin">move to sidebar</button> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-unpin-button" data-event-name="pinnable-header.vector-appearance.unpin">hide</button> </div> </div> </div> </nav> </div> </div> <div id="bodyContent" class="vector-body" aria-labelledby="firstHeading" data-mw-ve-target-container> <div class="vector-body-before-content"> <div class="mw-indicators"> </div> <div id="siteSub" class="noprint">From Wikipedia, the free encyclopedia</div> </div> <div id="contentSub"><div id="mw-content-subtitle"></div></div> <div id="mw-content-text" class="mw-body-content"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr"><p class="mw-empty-elt"> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Hardware-accelerated-molecular-modeling.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/4/48/Hardware-accelerated-molecular-modeling.png" decoding="async" width="180" height="154" class="mw-file-element" data-file-width="180" data-file-height="154" /></a><figcaption>Modeling of ionic liquid</figcaption></figure> <div class="shortdescription nomobile noexcerpt noprint searchaux" style="display:none">Discovering chemical properties by physical simulations</div> <p><b>Molecular modelling</b> encompasses all methods, theoretical and computational, used to <a href="/wiki/Model_(abstract)" class="mw-redirect" title="Model (abstract)">model</a> or mimic the behaviour of <a href="/wiki/Molecule" title="Molecule">molecules</a>.<sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> The methods are used in the fields of <a href="/wiki/Computational_chemistry" title="Computational chemistry">computational chemistry</a>, <a href="/wiki/Drug_design" title="Drug design">drug design</a>, <a href="/wiki/Computational_biology" title="Computational biology">computational biology</a> and <a href="/wiki/Materials_science" title="Materials science">materials science</a> to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a <a href="/wiki/Molecular_mechanics" title="Molecular mechanics">molecular mechanics</a> approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a <a href="/wiki/Quantum_chemistry" title="Quantum chemistry">quantum chemistry</a> approach). </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Molecular_mechanics">Molecular mechanics</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Molecular_modelling&action=edit&section=1" title="Edit section: Molecular mechanics"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size mw-halign-right" typeof="mw:File/Thumb"><a href="/wiki/File:Protein_backbone_PhiPsiOmega_drawing.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/9/97/Protein_backbone_PhiPsiOmega_drawing.svg/220px-Protein_backbone_PhiPsiOmega_drawing.svg.png" decoding="async" width="220" height="418" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/9/97/Protein_backbone_PhiPsiOmega_drawing.svg/330px-Protein_backbone_PhiPsiOmega_drawing.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/9/97/Protein_backbone_PhiPsiOmega_drawing.svg/440px-Protein_backbone_PhiPsiOmega_drawing.svg.png 2x" data-file-width="520" data-file-height="988" /></a><figcaption>The backbone <a href="/wiki/Dihedral_angle" title="Dihedral angle">dihedral angles</a> are included in the molecular model of a <a href="/wiki/Protein" title="Protein">protein</a>.</figcaption></figure> <p><a href="/wiki/Molecular_mechanics" title="Molecular mechanics">Molecular mechanics</a> is one aspect of molecular modelling, as it involves the use of <a href="/wiki/Classical_mechanics" title="Classical mechanics">classical mechanics</a> (<a href="/wiki/Newtonian_mechanics" class="mw-redirect" title="Newtonian mechanics">Newtonian mechanics</a>) to describe the physical basis behind the models. Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass. The interactions between neighbouring atoms are described by spring-like interactions (representing <a href="/wiki/Chemical_bond" title="Chemical bond">chemical bonds</a>) and <a href="/wiki/Van_der_Waals_force" title="Van der Waals force">Van der Waals forces</a>. The <a href="/wiki/Lennard-Jones_potential" title="Lennard-Jones potential">Lennard-Jones potential</a> is commonly used to describe the latter. The electrostatic interactions are computed based on <a href="/wiki/Coulomb%27s_law" title="Coulomb's law">Coulomb's law</a>. Atoms are assigned coordinates in Cartesian space or in <a href="/wiki/Internal_coordinates" class="mw-redirect" title="Internal coordinates">internal coordinates</a>, and can also be assigned velocities in dynamical simulations. The atomic velocities are related to the temperature of the system, a macroscopic quantity. The collective mathematical expression is termed a <a href="/wiki/Potential_function_(disambiguation)" class="mw-redirect mw-disambig" title="Potential function (disambiguation)">potential function</a> and is related to the system internal energy (U), a thermodynamic quantity equal to the sum of potential and kinetic energies. Methods which minimize the potential energy are termed energy minimization methods (e.g., <a href="/wiki/Steepest_descent" class="mw-redirect" title="Steepest descent">steepest descent</a> and <a href="/wiki/Conjugate_gradient" class="mw-redirect" title="Conjugate gradient">conjugate gradient</a>), while methods that model the behaviour of the system with propagation of time are termed <a href="/wiki/Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a>. </p> <dl><dd><span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle E=E_{\text{bonds}}+E_{\text{angle}}+E_{\text{dihedral}}+E_{\text{non-bonded}}\,}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <mi>E</mi> <mo>=</mo> <msub> <mi>E</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>bonds</mtext> </mrow> </msub> <mo>+</mo> <msub> <mi>E</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>angle</mtext> </mrow> </msub> <mo>+</mo> <msub> <mi>E</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>dihedral</mtext> </mrow> </msub> <mo>+</mo> <msub> <mi>E</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>non-bonded</mtext> </mrow> </msub> <mspace width="thinmathspace" /> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle E=E_{\text{bonds}}+E_{\text{angle}}+E_{\text{dihedral}}+E_{\text{non-bonded}}\,}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/5325ed5686a8aedb0a4734334023b4be55a68163" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -1.005ex; width:43.788ex; height:2.843ex;" alt="{\displaystyle E=E_{\text{bonds}}+E_{\text{angle}}+E_{\text{dihedral}}+E_{\text{non-bonded}}\,}"></span></dd></dl> <dl><dd><span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle E_{\text{non-bonded}}=E_{\text{electrostatic}}+E_{\text{van der Waals}}\,}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <msub> <mi>E</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>non-bonded</mtext> </mrow> </msub> <mo>=</mo> <msub> <mi>E</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>electrostatic</mtext> </mrow> </msub> <mo>+</mo> <msub> <mi>E</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>van der Waals</mtext> </mrow> </msub> <mspace width="thinmathspace" /> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle E_{\text{non-bonded}}=E_{\text{electrostatic}}+E_{\text{van der Waals}}\,}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/f6a489675b7c03d1d1c6a7e8512370f86b4369ba" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.671ex; width:39.756ex; height:2.509ex;" alt="{\displaystyle E_{\text{non-bonded}}=E_{\text{electrostatic}}+E_{\text{van der Waals}}\,}"></span></dd></dl> <p>This function, referred to as a <a href="/wiki/Potential_function_(disambiguation)" class="mw-redirect mw-disambig" title="Potential function (disambiguation)">potential function</a>, computes the molecular potential energy as a sum of energy terms that describe the deviation of bond lengths, bond angles and torsion angles away from equilibrium values, plus terms for non-bonded pairs of atoms describing van der Waals and electrostatic interactions. The set of parameters consisting of equilibrium bond lengths, bond angles, partial charge values, force constants and van der Waals parameters are collectively termed a <a href="/wiki/Force_field_(chemistry)" title="Force field (chemistry)">force field</a>. Different implementations of molecular mechanics use different mathematical expressions and different parameters for the <a href="/wiki/Potential_function_(disambiguation)" class="mw-redirect mw-disambig" title="Potential function (disambiguation)">potential function</a>.<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> The common force fields in use today have been developed by using chemical theory, experimental reference data, and high level quantum calculations. The method, termed energy minimization, is used to find positions of zero gradient for all atoms, in other words, a local energy minimum. Lower energy states are more stable and are commonly investigated because of their role in chemical and biological processes. A <a href="/wiki/Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a> simulation, on the other hand, computes the behaviour of a system as a function of time. It involves solving Newton's laws of motion, principally the second law, <span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle \mathbf {F} =m\mathbf {a} }"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <mrow class="MJX-TeXAtom-ORD"> <mi mathvariant="bold">F</mi> </mrow> <mo>=</mo> <mi>m</mi> <mrow class="MJX-TeXAtom-ORD"> <mi mathvariant="bold">a</mi> </mrow> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle \mathbf {F} =m\mathbf {a} }</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/d0c60fab89e8c3193952047dc565bcf8d233d115" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.338ex; width:8.121ex; height:2.176ex;" alt="{\displaystyle \mathbf {F} =m\mathbf {a} }"></span>. Integration of Newton's laws of motion, using different integration algorithms, leads to atomic trajectories in space and time. The force on an atom is defined as the negative gradient of the potential energy function. The energy minimization method is useful to obtain a static picture for comparing between states of similar systems, while molecular dynamics provides information about the dynamic processes with the intrinsic inclusion of temperature effects. </p> <div class="mw-heading mw-heading2"><h2 id="Variables">Variables</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Molecular_modelling&action=edit&section=2" title="Edit section: Variables"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Molecules can be modelled either in vacuum, or in the presence of a solvent such as water. Simulations of systems in vacuum are referred to as <i>gas-phase</i> simulations, while those that include the presence of solvent molecules are referred to as <i>explicit solvent</i> simulations. In another type of simulation, the effect of solvent is estimated using an empirical mathematical expression; these are termed <i>implicit solvation</i> simulations. </p> <div class="mw-heading mw-heading3"><h3 id="Coordinate_representations">Coordinate representations</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Molecular_modelling&action=edit&section=3" title="Edit section: Coordinate representations"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Most force fields are distance-dependent, making the most convenient expression for these Cartesian coordinates. Yet the comparatively rigid nature of bonds which occur between specific atoms, and in essence, defines what is meant by the designation <i>molecule</i>, make an internal coordinate system the most logical representation. In some fields the IC representation (bond length, angle between bonds, and twist angle of the bond as shown in the figure) is termed the <a href="/wiki/Z-matrix_(chemistry)" title="Z-matrix (chemistry)">Z-matrix</a> or torsion angle representation. Unfortunately, continuous motions in Cartesian space often require discontinuous angular branches in internal coordinates, making it relatively hard to work with force fields in the internal coordinate representation, and conversely a simple displacement of an atom in Cartesian space may not be a straight line trajectory due to the prohibitions of the interconnected bonds. Thus, it is very common for computational optimizing programs to flip back and forth between representations during their iterations. This can dominate the calculation time of the potential itself and in long chain molecules introduce cumulative numerical inaccuracy. While all conversion algorithms produce mathematically identical results, they differ in speed and numerical accuracy.<sup id="cite_ref-Parsons_2005_3-0" class="reference"><a href="#cite_note-Parsons_2005-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> Currently, the fastest and most accurate torsion to Cartesian conversion is the Natural Extension Reference Frame (NERF) method.<sup id="cite_ref-Parsons_2005_3-1" class="reference"><a href="#cite_note-Parsons_2005-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Applications">Applications</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Molecular_modelling&action=edit&section=4" title="Edit section: Applications"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Molecular modelling methods are used routinely to investigate the structure, dynamics, surface properties, and thermodynamics of inorganic, biological, and polymeric systems. A large number of molecular models of force field are today readily available in databases.<sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> The types of biological activity that have been investigated using molecular modelling include <a href="/wiki/Protein_folding" title="Protein folding">protein folding</a>, <a href="/wiki/Enzyme" title="Enzyme">enzyme</a> <a href="/wiki/Catalysis" title="Catalysis">catalysis</a>, protein stability, conformational changes associated with biomolecular function, and molecular recognition of proteins, <a href="/wiki/DNA" title="DNA">DNA</a>, and membrane complexes.<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Molecular_modelling&action=edit&section=5" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1184024115">.mw-parser-output .div-col{margin-top:0.3em;column-width:30em}.mw-parser-output .div-col-small{font-size:90%}.mw-parser-output .div-col-rules{column-rule:1px solid #aaa}.mw-parser-output .div-col dl,.mw-parser-output .div-col ol,.mw-parser-output .div-col ul{margin-top:0}.mw-parser-output .div-col li,.mw-parser-output .div-col dd{page-break-inside:avoid;break-inside:avoid-column}</style><div class="div-col" style="column-width: 22em;"> <ul><li><a href="/wiki/Cheminformatics" title="Cheminformatics">Cheminformatics</a></li> <li><a href="/wiki/Comparison_of_force_field_implementations" class="mw-redirect" title="Comparison of force field implementations">Comparison of force field implementations</a></li> <li><a href="/wiki/Comparison_of_nucleic_acid_simulation_software" title="Comparison of nucleic acid simulation software">Comparison of nucleic acid simulation software</a></li> <li><a href="/wiki/Comparison_of_software_for_molecular_mechanics_modeling" title="Comparison of software for molecular mechanics modeling">Comparison of software for molecular mechanics modeling</a></li> <li><a href="/wiki/Density_functional_theory#Software_supporting_DFT" title="Density functional theory">Density functional theory</a> software</li> <li><a href="/wiki/List_of_molecular_graphics_systems" title="List of molecular graphics systems">List of molecular graphics systems</a></li> <li><a href="/wiki/List_of_protein_structure_prediction_software" title="List of protein structure prediction software">List of protein structure prediction software</a></li> <li><a href="/wiki/List_of_software_for_Monte_Carlo_molecular_modeling" title="List of software for Monte Carlo molecular modeling">List of software for Monte Carlo molecular modeling</a></li> <li><a href="/wiki/List_of_software_for_nanostructures_modeling" title="List of software for nanostructures modeling">List of software for nanostructures modeling</a></li> <li><a href="/wiki/Molecular_design_software" title="Molecular design software">Molecular design software</a></li> <li><a href="/wiki/Molecular_engineering" title="Molecular engineering">Molecular engineering</a></li> <li><a href="/wiki/Molecular_graphics" title="Molecular graphics">Molecular graphics</a></li> <li><a href="/wiki/Molecular_model" title="Molecular model">Molecular model</a></li> <li><a href="/wiki/Molecular_modeling_on_GPU" class="mw-redirect" title="Molecular modeling on GPU">Molecular modeling on GPU</a></li> <li><a href="/wiki/Molecule_editor" title="Molecule editor">Molecule editor</a></li> <li><a href="/wiki/Monte_Carlo_method" title="Monte Carlo method">Monte Carlo method</a></li> <li><a href="/wiki/Quantum_chemistry_computer_programs" class="mw-redirect" title="Quantum chemistry computer programs">Quantum chemistry computer programs</a></li> <li><a href="/wiki/Semi-empirical_quantum_chemistry_method" title="Semi-empirical quantum chemistry method">Semi-empirical quantum chemistry method</a></li> <li><a href="/wiki/Simulated_reality" title="Simulated reality">Simulated reality</a></li> <li><a href="/wiki/Structural_bioinformatics" title="Structural bioinformatics">Structural bioinformatics</a></li> <li><a href="/wiki/Z-matrix_(mathematics)" title="Z-matrix (mathematics)">Z-matrix (mathematics)</a></li></ul></div> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Molecular_modelling&action=edit&section=6" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist"> <div class="mw-references-wrap"><ol class="references"> <li id="cite_note-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-1">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFLeach2009" class="citation book cs1">Leach AR (2009). <i>Molecular modelling : principles and applications</i>. Pearson Prentice Hall. <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/978-0-582-38210-7" title="Special:BookSources/978-0-582-38210-7"><bdi>978-0-582-38210-7</bdi></a>. <a href="/wiki/OCLC_(identifier)" class="mw-redirect" title="OCLC (identifier)">OCLC</a> <a rel="nofollow" class="external text" href="https://search.worldcat.org/oclc/635267533">635267533</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Molecular+modelling+%3A+principles+and+applications&rft.pub=Pearson+Prentice+Hall&rft.date=2009&rft_id=info%3Aoclcnum%2F635267533&rft.isbn=978-0-582-38210-7&rft.aulast=Leach&rft.aufirst=Andrew+R.&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></span> </li> <li id="cite_note-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-2">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFHeinzRamezani-Dakhel2016" class="citation journal cs1">Heinz H, Ramezani-Dakhel H (January 2016). <a rel="nofollow" class="external text" href="http://xlink.rsc.org/?DOI=C5CS00890E">"Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities"</a>. <i>Chemical Society Reviews</i>. <b>45</b> (2): 412–48. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1039%2FC5CS00890E">10.1039/C5CS00890E</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/26750724">26750724</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Chemical+Society+Reviews&rft.atitle=Simulations+of+inorganic-bioorganic+interfaces+to+discover+new+materials%3A+insights%2C+comparisons+to+experiment%2C+challenges%2C+and+opportunities&rft.volume=45&rft.issue=2&rft.pages=412-48&rft.date=2016-01&rft_id=info%3Adoi%2F10.1039%2FC5CS00890E&rft_id=info%3Apmid%2F26750724&rft.aulast=Heinz&rft.aufirst=H&rft.au=Ramezani-Dakhel%2C+H&rft_id=http%3A%2F%2Fxlink.rsc.org%2F%3FDOI%3DC5CS00890E&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></span> </li> <li id="cite_note-Parsons_2005-3"><span class="mw-cite-backlink">^ <a href="#cite_ref-Parsons_2005_3-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-Parsons_2005_3-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFParsonsHolmesRojasTsai2005" class="citation journal cs1">Parsons J, Holmes JB, Rojas JM, Tsai J, Strauss CE (July 2005). 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Ilja (2014-01-02). <a rel="nofollow" class="external text" href="https://www.tandfonline.com/doi/full/10.1080/08927022.2013.842994">"An online parameter and property database for the TraPPE force field"</a>. <i>Molecular Simulation</i>. <b>40</b> (1–3): 101–105. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1080%2F08927022.2013.842994">10.1080/08927022.2013.842994</a>. <a href="/wiki/ISSN_(identifier)" class="mw-redirect" title="ISSN (identifier)">ISSN</a> <a rel="nofollow" class="external text" href="https://search.worldcat.org/issn/0892-7022">0892-7022</a>. <a href="/wiki/S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:95716947">95716947</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Molecular+Simulation&rft.atitle=An+online+parameter+and+property+database+for+the+TraPPE+force+field&rft.volume=40&rft.issue=1%E2%80%933&rft.pages=101-105&rft.date=2014-01-02&rft_id=https%3A%2F%2Fapi.semanticscholar.org%2FCorpusID%3A95716947%23id-name%3DS2CID&rft.issn=0892-7022&rft_id=info%3Adoi%2F10.1080%2F08927022.2013.842994&rft.aulast=Eggimann&rft.aufirst=Becky+L.&rft.au=Sunnarborg%2C+Amara+J.&rft.au=Stern%2C+Hudson+D.&rft.au=Bliss%2C+Andrew+P.&rft.au=Siepmann%2C+J.+Ilja&rft_id=https%3A%2F%2Fwww.tandfonline.com%2Fdoi%2Ffull%2F10.1080%2F08927022.2013.842994&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></span> </li> <li id="cite_note-6"><span class="mw-cite-backlink"><b><a href="#cite_ref-6">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFLeeChengSwailsYeom2016" class="citation journal cs1">Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, et al. (January 2016). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712441">"CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field"</a>. <i>Journal of Chemical Theory and Computation</i>. <b>12</b> (1): 405–13. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1021%2Facs.jctc.5b00935">10.1021/acs.jctc.5b00935</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712441">4712441</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/26631602">26631602</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Journal+of+Chemical+Theory+and+Computation&rft.atitle=CHARMM-GUI+Input+Generator+for+NAMD%2C+GROMACS%2C+AMBER%2C+OpenMM%2C+and+CHARMM%2FOpenMM+Simulations+Using+the+CHARMM36+Additive+Force+Field&rft.volume=12&rft.issue=1&rft.pages=405-13&rft.date=2016-01&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4712441%23id-name%3DPMC&rft_id=info%3Apmid%2F26631602&rft_id=info%3Adoi%2F10.1021%2Facs.jctc.5b00935&rft.aulast=Lee&rft.aufirst=J&rft.au=Cheng%2C+X&rft.au=Swails%2C+JM&rft.au=Yeom%2C+MS&rft.au=Eastman%2C+PK&rft.au=Lemkul%2C+JA&rft.au=Wei%2C+S&rft.au=Buckner%2C+J&rft.au=Jeong%2C+JC&rft.au=Qi%2C+Y&rft.au=Jo%2C+S&rft.au=Pande%2C+VS&rft.au=Case%2C+DA&rft.au=Brooks%2C+CL&rft.au=MacKerell%2C+AD&rft.au=Klauda%2C+JB&rft.au=Im%2C+W&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4712441&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></span> </li> </ol></div></div> <div class="mw-heading mw-heading2"><h2 id="Further_reading">Further reading</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Molecular_modelling&action=edit&section=7" title="Edit section: Further reading"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239549316">.mw-parser-output .refbegin{margin-bottom:0.5em}.mw-parser-output .refbegin-hanging-indents>ul{margin-left:0}.mw-parser-output .refbegin-hanging-indents>ul>li{margin-left:0;padding-left:3.2em;text-indent:-3.2em}.mw-parser-output .refbegin-hanging-indents ul,.mw-parser-output .refbegin-hanging-indents ul li{list-style:none}@media(max-width:720px){.mw-parser-output .refbegin-hanging-indents>ul>li{padding-left:1.6em;text-indent:-1.6em}}.mw-parser-output .refbegin-columns{margin-top:0.3em}.mw-parser-output .refbegin-columns ul{margin-top:0}.mw-parser-output .refbegin-columns li{page-break-inside:avoid;break-inside:avoid-column}@media screen{.mw-parser-output .refbegin{font-size:90%}}</style><div class="refbegin" style=""> <ul><li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFAllenTildesley1989" class="citation book cs1">Allen MP, Tildesley DJ (1989). <i>Computer simulation of liquids</i>. Oxford University Press. <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/0-19-855645-4" title="Special:BookSources/0-19-855645-4"><bdi>0-19-855645-4</bdi></a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Computer+simulation+of+liquids&rft.pub=Oxford+University+Press&rft.date=1989&rft.isbn=0-19-855645-4&rft.aulast=Allen&rft.aufirst=MP&rft.au=Tildesley%2C+DJ&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></li> <li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFFrenkelSmit1996" class="citation book cs1">Frenkel D, Smit B (1996). <i>Understanding Molecular Simulation: From Algorithms to Applications</i>. Academic Press. <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/0-12-267370-0" title="Special:BookSources/0-12-267370-0"><bdi>0-12-267370-0</bdi></a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Understanding+Molecular+Simulation%3A+From+Algorithms+to+Applications&rft.pub=Academic+Press&rft.date=1996&rft.isbn=0-12-267370-0&rft.aulast=Frenkel&rft.aufirst=D&rft.au=Smit%2C+B&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></li> <li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFRapaport2004" class="citation book cs1">Rapaport DC (2004). <i>The Art of Molecular Dynamics Simulation</i>. Cambridge University Press. <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/0-521-82568-7" title="Special:BookSources/0-521-82568-7"><bdi>0-521-82568-7</bdi></a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=The+Art+of+Molecular+Dynamics+Simulation&rft.pub=Cambridge+University+Press&rft.date=2004&rft.isbn=0-521-82568-7&rft.aulast=Rapaport&rft.aufirst=DC&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></li> <li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFSadus2002" class="citation book cs1">Sadus RJ (2002). <i>Molecular Simulation of Fluids: Theory, Algorithms and Object-Orientation</i>. Elsevier. <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/0-444-51082-6" title="Special:BookSources/0-444-51082-6"><bdi>0-444-51082-6</bdi></a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Molecular+Simulation+of+Fluids%3A+Theory%2C+Algorithms+and+Object-Orientation&rft.pub=Elsevier&rft.date=2002&rft.isbn=0-444-51082-6&rft.aulast=Sadus&rft.aufirst=RJ&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></li> <li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFRamachandranDeepaKrishnan_Namboori2008" class="citation book cs1">Ramachandran KI, Deepa G, Krishnan Namboori PK (2008). <a rel="nofollow" class="external text" href="http://www.amrita.edu/publication/computational-chemistry-and-molecular-modeling"><i>Computational Chemistry and Molecular Modeling Principles and Applications</i></a>. Springer-Verlag GmbH. <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/978-3-540-77302-3" title="Special:BookSources/978-3-540-77302-3"><bdi>978-3-540-77302-3</bdi></a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Computational+Chemistry+and+Molecular+Modeling+Principles+and+Applications&rft.pub=Springer-Verlag+GmbH&rft.date=2008&rft.isbn=978-3-540-77302-3&rft.aulast=Ramachandran&rft.aufirst=KI&rft.au=Deepa%2C+G&rft.au=Krishnan+Namboori%2C+PK&rft_id=http%3A%2F%2Fwww.amrita.edu%2Fpublication%2Fcomputational-chemistry-and-molecular-modeling&rfr_id=info%3Asid%2Fen.wikipedia.org%3AMolecular+modelling" class="Z3988"></span></li></ul> </div><div class="navbox-styles"><style data-mw-deduplicate="TemplateStyles:r1129693374">.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output .hlist ul{margin:0;padding:0}.mw-parser-output .hlist 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href="/wiki/Template:Branches_of_chemistry" title="Template:Branches of chemistry"><abbr title="View this template">v</abbr></a></li><li class="nv-talk"><a href="/wiki/Template_talk:Branches_of_chemistry" title="Template talk:Branches of chemistry"><abbr title="Discuss this template">t</abbr></a></li><li class="nv-edit"><a href="/wiki/Special:EditPage/Template:Branches_of_chemistry" title="Special:EditPage/Template:Branches of chemistry"><abbr title="Edit this template">e</abbr></a></li></ul></div><div id="Branches_of_chemistry" style="font-size:114%;margin:0 4em">Branches of <a href="/wiki/Chemistry" title="Chemistry">chemistry</a></div></th></tr><tr><td class="navbox-abovebelow" colspan="2"><div> <ul><li><a href="/wiki/Glossary_of_chemical_formulae" title="Glossary of chemical formulae">Glossary of chemical formulae</a></li> <li><a href="/wiki/List_of_biomolecules" title="List of biomolecules">List of biomolecules</a></li> <li><a href="/wiki/List_of_inorganic_compounds" title="List of inorganic compounds">List of inorganic compounds</a></li> <li><a href="/wiki/Periodic_table" title="Periodic table">Periodic table</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Analytical_chemistry" title="Analytical chemistry">Analytical</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Instrumental_chemistry" title="Instrumental chemistry">Instrumental chemistry</a></li> <li><a href="/wiki/Electroanalytical_methods" title="Electroanalytical methods">Electroanalytical methods</a></li> <li><a href="/wiki/Spectroscopy" title="Spectroscopy">Spectroscopy</a> <ul><li><a href="/wiki/Infrared_spectroscopy" title="Infrared spectroscopy">IR</a></li> <li><a href="/wiki/Raman_spectroscopy" title="Raman spectroscopy">Raman</a></li> <li><a href="/wiki/Ultraviolet%E2%80%93visible_spectroscopy" title="Ultraviolet–visible spectroscopy">UV-Vis</a></li> <li><a href="/wiki/Nuclear_magnetic_resonance_spectroscopy" title="Nuclear magnetic resonance spectroscopy">NMR</a></li></ul></li> <li><a href="/wiki/Mass_spectrometry" title="Mass spectrometry">Mass spectrometry</a> <ul><li><a href="/wiki/Electron_ionization" title="Electron ionization">EI</a></li> <li><a href="/wiki/Inductively_coupled_plasma_mass_spectrometry" title="Inductively coupled plasma mass spectrometry">ICP</a></li> <li><a href="/wiki/Matrix-assisted_laser_desorption/ionization" title="Matrix-assisted laser desorption/ionization">MALDI</a></li></ul></li> <li><a href="/wiki/Separation_process" title="Separation process">Separation process</a></li> <li><a href="/wiki/Chromatography" title="Chromatography">Chromatography</a> <ul><li><a href="/wiki/Gas_chromatography" title="Gas chromatography">GC</a></li> <li><a href="/wiki/High-performance_liquid_chromatography" title="High-performance liquid chromatography">HPLC</a></li></ul></li> <li><a href="/wiki/Crystallography" title="Crystallography">Crystallography</a></li> <li><a href="/wiki/Characterization_(materials_science)" title="Characterization (materials science)">Characterization</a></li> <li><a href="/wiki/Titration" title="Titration">Titration</a></li> <li><a href="/wiki/Wet_chemistry" title="Wet chemistry">Wet chemistry</a></li> <li><a href="/wiki/Calorimetry" title="Calorimetry">Calorimetry</a></li> <li><a href="/wiki/Elemental_analysis" title="Elemental analysis">Elemental analysis</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Theoretical_chemistry" title="Theoretical chemistry">Theoretical</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Quantum_chemistry" title="Quantum chemistry">Quantum chemistry</a></li> <li><a href="/wiki/Computational_chemistry" title="Computational chemistry">Computational chemistry</a> <ul><li><a href="/wiki/Mathematical_chemistry" title="Mathematical chemistry">Mathematical chemistry</a></li></ul></li> <li><a class="mw-selflink selflink">Molecular modelling</a></li> <li><a href="/wiki/Molecular_mechanics" title="Molecular mechanics">Molecular mechanics</a></li> <li><a href="/wiki/Molecular_dynamics" title="Molecular dynamics">Molecular dynamics</a></li> <li><a href="/wiki/Molecular_geometry" title="Molecular geometry">Molecular geometry</a> <ul><li><a href="/wiki/VSEPR_theory" title="VSEPR theory">VSEPR theory</a></li></ul></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Physical_chemistry" title="Physical chemistry">Physical</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Electrochemistry" title="Electrochemistry">Electrochemistry</a> <ul><li><a href="/wiki/Spectroelectrochemistry" title="Spectroelectrochemistry">Spectroelectrochemistry</a></li> <li><a href="/wiki/Photoelectrochemistry" title="Photoelectrochemistry">Photoelectrochemistry</a></li></ul></li> <li><a href="/wiki/Thermochemistry" title="Thermochemistry">Thermochemistry</a></li> <li><a href="/wiki/Chemical_thermodynamics" title="Chemical thermodynamics">Chemical thermodynamics</a></li> <li><a href="/wiki/Surface_science" title="Surface science">Surface science</a></li> <li><a href="/wiki/Interface_and_colloid_science" title="Interface and colloid science">Interface and colloid science</a> <ul><li><a href="/wiki/Micromeritics" title="Micromeritics">Micromeritics</a></li></ul></li> <li><a href="/wiki/Cryochemistry" title="Cryochemistry">Cryochemistry</a></li> <li><a href="/wiki/Sonochemistry" title="Sonochemistry">Sonochemistry</a></li> <li><a href="/wiki/Structural_chemistry" title="Structural chemistry">Structural chemistry</a></li> <li><a href="/wiki/Chemical_physics" title="Chemical physics">Chemical physics</a> <ul><li><a href="/wiki/Molecular_physics" title="Molecular physics">Molecular physics</a></li></ul></li> <li><a href="/wiki/Femtochemistry" title="Femtochemistry">Femtochemistry</a></li> <li><a href="/wiki/Chemical_kinetics" title="Chemical kinetics">Chemical kinetics</a></li> <li><a href="/wiki/Spectroscopy" title="Spectroscopy">Spectroscopy</a></li> <li><a href="/wiki/Photochemistry" title="Photochemistry">Photochemistry</a></li> <li><a href="/wiki/Spin_chemistry" title="Spin chemistry">Spin chemistry</a></li> <li><a href="/wiki/Microwave_chemistry" title="Microwave chemistry">Microwave chemistry</a></li> <li><a href="/wiki/Equilibrium_chemistry" title="Equilibrium chemistry">Equilibrium chemistry</a></li> <li><a href="/wiki/Mechanochemistry" title="Mechanochemistry">Mechanochemistry</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Inorganic_chemistry" title="Inorganic chemistry">Inorganic</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Coordination_complex" title="Coordination complex">Coordination chemistry</a></li> <li><a href="/wiki/Magnetochemistry" title="Magnetochemistry">Magnetochemistry</a></li> <li><a href="/wiki/Organometallic_chemistry" title="Organometallic chemistry">Organometallic chemistry</a> <ul><li><a href="/wiki/Organolanthanide_chemistry" title="Organolanthanide chemistry">Organolanthanide chemistry</a></li></ul></li> <li><a href="/wiki/Atom_cluster" class="mw-redirect" title="Atom cluster">Cluster chemistry</a></li> <li><a href="/wiki/Solid-state_chemistry" title="Solid-state chemistry">Solid-state chemistry</a></li> <li><a href="/wiki/Ceramic_chemistry" class="mw-redirect" title="Ceramic chemistry">Ceramic chemistry</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Organic_chemistry" title="Organic chemistry">Organic</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Stereochemistry" title="Stereochemistry">Stereochemistry</a> <ul><li><a href="/wiki/Alkane_stereochemistry" class="mw-redirect" title="Alkane stereochemistry">Alkane stereochemistry</a></li></ul></li> <li><a href="/wiki/Physical_organic_chemistry" title="Physical organic chemistry">Physical organic chemistry</a></li> <li><a href="/wiki/Organic_reactions" class="mw-redirect" title="Organic reactions">Organic reactions</a></li> <li><a href="/wiki/Organic_synthesis" title="Organic synthesis">Organic synthesis</a></li> <li><a href="/wiki/Retrosynthetic_analysis" title="Retrosynthetic analysis">Retrosynthetic analysis</a></li> <li><a href="/wiki/Enantioselective_synthesis" title="Enantioselective synthesis">Enantioselective synthesis</a></li> <li><a href="/wiki/Total_synthesis" title="Total synthesis">Total synthesis</a> / <a href="/wiki/Semisynthesis" title="Semisynthesis">Semisynthesis</a></li> <li><a href="/wiki/Fullerene_chemistry" title="Fullerene chemistry">Fullerene chemistry</a></li> <li><a href="/wiki/Polymer_chemistry" title="Polymer chemistry">Polymer chemistry</a></li> <li><a href="/wiki/Petrochemistry" class="mw-redirect" title="Petrochemistry">Petrochemistry</a></li> <li><a href="/wiki/Dynamic_covalent_chemistry" title="Dynamic covalent chemistry">Dynamic covalent chemistry</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Biochemistry" title="Biochemistry">Biological</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Biochemistry" title="Biochemistry">Biochemistry</a> <ul><li><a href="/wiki/Molecular_biology" title="Molecular biology">Molecular biology</a></li> <li><a href="/wiki/Cell_biology" title="Cell biology">Cell biology</a></li></ul></li> <li><a href="/wiki/Chemical_biology" title="Chemical biology">Chemical biology</a> <ul><li><a href="/wiki/Bioorthogonal_chemistry" title="Bioorthogonal chemistry">Bioorthogonal chemistry</a></li></ul></li> <li><a href="/wiki/Medicinal_chemistry" title="Medicinal chemistry">Medicinal chemistry</a> <ul><li><a href="/wiki/Pharmacology" title="Pharmacology">Pharmacology</a></li></ul></li> <li><a href="/wiki/Clinical_chemistry" title="Clinical chemistry">Clinical chemistry</a></li> <li><a href="/wiki/Neurochemistry" title="Neurochemistry">Neurochemistry</a></li> <li><a href="/wiki/Bioorganic_chemistry" title="Bioorganic chemistry">Bioorganic chemistry</a></li> <li><a href="/wiki/Bioorganometallic_chemistry" title="Bioorganometallic chemistry">Bioorganometallic chemistry</a></li> <li><a href="/wiki/Bioinorganic_chemistry" title="Bioinorganic chemistry">Bioinorganic chemistry</a></li> <li><a href="/wiki/Biophysical_chemistry" title="Biophysical chemistry">Biophysical chemistry</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Interdisciplinarity" title="Interdisciplinarity">Interdisciplinarity</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Nuclear_chemistry" title="Nuclear chemistry">Nuclear chemistry</a> <ul><li><a href="/wiki/Radiochemistry" title="Radiochemistry">Radiochemistry</a></li> <li><a href="/wiki/Radiation_chemistry" title="Radiation chemistry">Radiation chemistry</a></li> <li><a href="/wiki/Actinide_chemistry" title="Actinide chemistry">Actinide chemistry</a></li></ul></li> <li><a href="/wiki/Cosmochemistry" title="Cosmochemistry">Cosmochemistry</a> / <a href="/wiki/Astrochemistry" title="Astrochemistry">Astrochemistry</a> / <a href="/wiki/Stellar_chemistry" title="Stellar chemistry">Stellar chemistry</a></li> <li><a href="/wiki/Geochemistry" title="Geochemistry">Geochemistry</a> <ul><li><a href="/wiki/Biogeochemistry" title="Biogeochemistry">Biogeochemistry</a></li> <li><a href="/wiki/Photogeochemistry" title="Photogeochemistry">Photogeochemistry</a></li></ul></li></ul> <ul><li><a href="/wiki/Environmental_chemistry" title="Environmental chemistry">Environmental chemistry</a> <ul><li><a href="/wiki/Atmospheric_chemistry" title="Atmospheric chemistry">Atmospheric chemistry</a></li> <li><a href="/wiki/Ocean_chemistry" class="mw-redirect" title="Ocean chemistry">Ocean chemistry</a></li></ul></li> <li><a href="/wiki/Clay_chemistry" title="Clay chemistry">Clay chemistry</a></li> <li><a href="/wiki/Carbochemistry" title="Carbochemistry">Carbochemistry</a></li> <li><a href="/wiki/Food_chemistry" title="Food chemistry">Food chemistry</a> <ul><li><a href="/wiki/Carbohydrate_chemistry" class="mw-redirect" title="Carbohydrate chemistry">Carbohydrate chemistry</a></li> <li><a href="/wiki/Food_physical_chemistry" title="Food physical chemistry">Food physical chemistry</a></li></ul></li> <li><a href="/wiki/Agricultural_chemistry" title="Agricultural chemistry">Agricultural chemistry</a> <ul><li><a href="/wiki/Soil_chemistry" title="Soil chemistry">Soil chemistry</a></li></ul></li></ul> <ul><li><a href="/wiki/Chemistry_education" title="Chemistry education">Chemistry education</a> <ul><li><a href="/wiki/Amateur_chemistry" title="Amateur chemistry">Amateur chemistry</a></li> <li><a href="/wiki/General_chemistry" title="General chemistry">General chemistry</a></li></ul></li> <li><a href="/wiki/Clandestine_chemistry" title="Clandestine chemistry">Clandestine chemistry</a></li> <li><a href="/wiki/Forensic_chemistry" title="Forensic chemistry">Forensic chemistry</a> <ul><li><a href="/wiki/Forensic_toxicology" title="Forensic toxicology">Forensic toxicology</a></li> <li><a href="/wiki/Post-mortem_chemistry" title="Post-mortem chemistry">Post-mortem chemistry</a></li></ul></li></ul> <ul><li><a href="/wiki/Nanochemistry" title="Nanochemistry">Nanochemistry</a> <ul><li><a href="/wiki/Supramolecular_chemistry" title="Supramolecular chemistry">Supramolecular chemistry</a></li></ul></li> <li><a href="/wiki/Chemical_synthesis" title="Chemical synthesis">Chemical synthesis</a> <ul><li><a href="/wiki/Green_chemistry" title="Green chemistry">Green chemistry</a></li> <li><a href="/wiki/Click_chemistry" title="Click chemistry">Click chemistry</a></li> <li><a href="/wiki/Combinatorial_chemistry" title="Combinatorial chemistry">Combinatorial chemistry</a></li> <li><a href="/wiki/Biosynthesis" title="Biosynthesis">Biosynthesis</a></li></ul></li> <li><a href="/wiki/Chemical_engineering" title="Chemical engineering">Chemical engineering</a> <ul><li><a href="/wiki/Stoichiometry" title="Stoichiometry">Stoichiometry</a></li></ul></li> <li><a href="/wiki/Materials_science" title="Materials science">Materials science</a> <ul><li><a href="/wiki/Metallurgy" title="Metallurgy">Metallurgy</a></li> <li><a href="/wiki/Ceramic_engineering" title="Ceramic engineering">Ceramic engineering</a></li> <li><a href="/wiki/Polymer_science" title="Polymer science">Polymer science</a></li></ul></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">See also</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/History_of_chemistry" title="History of chemistry">History of chemistry</a></li> <li><a href="/wiki/Nobel_Prize_in_Chemistry" title="Nobel Prize in Chemistry">Nobel Prize in Chemistry</a></li> <li><a href="/wiki/Timeline_of_chemistry" title="Timeline of chemistry">Timeline of chemistry</a> <ul><li><a href="/wiki/Discovery_of_chemical_elements" title="Discovery of chemical elements">of element discoveries</a></li></ul></li> <li>"<a href="/wiki/The_central_science" title="The central science">The central science</a>"</li> <li><a href="/wiki/Chemical_reaction" title="Chemical reaction">Chemical reaction</a> <ul><li><a href="/wiki/Catalysis" title="Catalysis">Catalysis</a></li></ul></li> <li><a href="/wiki/Chemical_element" title="Chemical element">Chemical element</a></li> <li><a href="/wiki/Chemical_compound" title="Chemical compound">Chemical compound</a></li> <li><a href="/wiki/Atom" title="Atom">Atom</a></li> <li><a href="/wiki/Molecule" title="Molecule">Molecule</a></li> <li><a href="/wiki/Ion" title="Ion">Ion</a></li> <li><a href="/wiki/Chemical_substance" title="Chemical substance">Chemical substance</a></li> <li><a href="/wiki/Chemical_bond" title="Chemical bond">Chemical bond</a></li> <li><a href="/wiki/Alchemy" title="Alchemy">Alchemy</a></li> <li><a href="/wiki/Quantum_mechanics" title="Quantum mechanics">Quantum mechanics</a></li></ul> </div></td></tr><tr><td class="navbox-abovebelow" colspan="2"><div> <ul><li><span class="noviewer" typeof="mw:File"><span title="Category"><img alt="" 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