SherbyNet - /page/wikibook/entry.mu

<!DOCTYPE html>

<title>CHARMM</title>

</head>

<span id="openzim-page-title" class="mw-page-title-main"><span class="mw-page-title-main">CHARMM</span></span>

</h1>

</header>

/* start https://en.wikipedia.org/ */

.mw-parser-output .infobox-subbox{padding:0;border:none;margin:-3px;width:auto;min-width:100%;font-size:100%;clear:none;float:none;background-color:transparent}.mw-parser-output .infobox-3cols-child{margin:auto}.mw-parser-output .infobox .navbar{font-size:100%}@media screen{html.skin-theme-clientpref-night .mw-parser-output .infobox-full-data:not(.notheme)>div:not(.notheme)[style]{background:#1f1f23!important;color:#f8f9fa}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .infobox-full-data:not(.notheme)>div:not(.notheme)[style]{background:#1f1f23!important;color:#f8f9fa}}@media(min-width:640px){body.skin--responsive .mw-parser-output .infobox-table{display:table!important}body.skin--responsive .mw-parser-output .infobox-table>caption{display:table-caption!important}body.skin--responsive .mw-parser-output .infobox-table>tbody{display:table-row-group}body.skin--responsive .mw-parser-output .infobox-table th,body.skin--responsive .mw-parser-output .infobox-table td{padding-left:inherit;padding-right:inherit}}

/* end https://en.wikipedia.org/ */

</style><table class="infobox vevent"><tbody><tr><th colspan="2" class="infobox-above summary">CHARMM</th></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Programmer" title="Programmer">Developer(s)</a></th><td class="infobox-data"><a href="Martin_Karplus" title="Martin Karplus">Martin Karplus</a>, <a href="Accelrys" class="mw-redirect" title="Accelrys">Accelrys</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Initial release</th><td class="infobox-data">1983<span style="display:none"> (<span class="bday dtstart published updated">1983</span>)</span></td></tr><tr style="display: none;"><td colspan="2" class="infobox-full-data"></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_release_life_cycle" title="Software release life cycle">Stable release</a></th><td class="infobox-data"><div style="margin:0px;">c47b1

/ 2022<span style="display:none"> (<span class="bday dtstart published updated">2022</span>)</span><sup id="cite_ref-versions_1-0" class="reference"><a href="#cite_note-versions-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup></div></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_release_life_cycle#Beta" title="Software release life cycle">Preview release</a></th><td class="infobox-data"><div style="margin:0px;">c48a1

/ 2022<span style="display:none"> (<span class="bday dtstart published updated">2022</span>)</span><sup id="cite_ref-versions_1-1" class="reference"><a href="#cite_note-versions-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup></div></td></tr><tr style="display:none"><td colspan="2">

</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Written in</th><td class="infobox-data"><a href="FORTRAN" class="mw-redirect" title="FORTRAN">FORTRAN</a> 77-95, <a href="CUDA" title="CUDA">CUDA</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Operating_system" title="Operating system">Operating system</a></th><td class="infobox-data"><a href="Unix-like" title="Unix-like">Unix-like</a>: <a href="Linux" title="Linux">Linux</a>, <a href="MacOS" title="MacOS">macOS</a>, <a href="IBM_AIX" title="IBM AIX">AIX</a>, <a href="IOS" title="IOS">iOS</a><sup id="cite_ref-OS+platforms_2-0" class="reference"><a href="#cite_note-OS+platforms-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Computing_platform" title="Computing platform">Platform</a></th><td class="infobox-data"><a href="X86" title="X86">x86</a>, <a href="ARM_architecture" class="mw-redirect" title="ARM architecture">ARM</a>, <a href="Nvidia" title="Nvidia">Nvidia</a> <a href="Graphics_processing_unit" title="Graphics processing unit">GPU</a>; <a href="Cray" title="Cray">Cray</a> <a href="Cray_XT4" title="Cray XT4">XT4</a>, <a href="Cray_XT5" title="Cray XT5">XT5</a><sup id="cite_ref-OS+platforms_2-1" class="reference"><a href="#cite_note-OS+platforms-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Available in</th><td class="infobox-data">English</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_categories#Categorization_approaches" title="Software categories">Type</a></th><td class="infobox-data"><a href="Molecular_dynamics" title="Molecular dynamics">Molecular dynamics</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_license" title="Software license">License</a></th><td class="infobox-data"><a href="Proprietary_software" title="Proprietary software">Proprietary</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="https://www.academiccharmm.org/">www<wbr>.academiccharmm<wbr>.org</a></span></td></tr></tbody></table>

<p><b>Chemistry at Harvard Macromolecular Mechanics</b> (<b>CHARMM</b>) is the name of a widely used set of <a href="Force_field_(chemistry)" title="Force field (chemistry)">force fields</a> for <a href="Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a>, and the name for the molecular dynamics simulation and analysis computer <a href="Software" title="Software">software</a> package associated with them.<sup id="cite_ref-Brooks1983_3-0" class="reference"><a href="#cite_note-Brooks1983-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup><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 CHARMM Development Project involves a worldwide network of developers working with <a href="Martin_Karplus" title="Martin Karplus">Martin Karplus</a> and his group at <a href="Harvard" class="mw-redirect" title="Harvard">Harvard</a> to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.

</p>

<div class="mw-heading mw-heading2"><h2 id="Force_fields">Force fields</h2></div>

<p>The CHARMM <a href="Force_field_(chemistry)" title="Force field (chemistry)">force fields</a> for proteins include: united-atom (sometimes termed <i>extended atom</i>) CHARMM19,<sup id="cite_ref-Reiher1985_6-0" class="reference"><a href="#cite_note-Reiher1985-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> all-atom CHARMM22<sup id="cite_ref-MacKerell1998_7-0" class="reference"><a href="#cite_note-MacKerell1998-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF.<sup id="cite_ref-MacKerell2004a_8-0" class="reference"><a href="#cite_note-MacKerell2004a-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermore, CHARMM22 is parametrized for the TIP3P explicit <a href="Water_model" title="Water model">water model</a>. Nevertheless, it is often used with <a href="Implicit_solvent" class="mw-redirect" title="Implicit solvent">implicit solvents</a>. In 2006, a special version of CHARMM22/CMAP was reparametrized for consistent use with implicit solvent GBSW.<sup id="cite_ref-Brooks2006_9-0" class="reference"><a href="#cite_note-Brooks2006-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup>

</p><p>The CHARMM22 force field has the following potential energy function:<sup id="cite_ref-MacKerell1998_7-1" class="reference"><a href="#cite_note-MacKerell1998-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-10" class="reference"><a href="#cite_note-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup>

</p><p><span class="mwe-math-element mwe-math-element-inline"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle {\begin{aligned}V=&\sum _{bonds}k_{b}(b-b_{0})^{2}+\sum _{angles}k_{\theta }(\theta -\theta _{0})^{2}+\sum _{dihedrals}k_{\phi }[1+\cos(n\phi -\delta )]\\&+\sum _{impropers}k_{\omega }(\omega -\omega _{0})^{2}+\sum _{Urey-Bradley}k_{u}(u-u_{0})^{2}\\&+\sum _{nonbonded}\left(\epsilon _{ij}\left[\left({\frac {R_{min_{ij}}}{r_{ij}}}\right)^{12}-2\left({\frac {R_{min_{ij}}}{r_{ij}}}\right)^{6}\right]+{\frac {q_{i}q_{j}}{\epsilon _{r}r_{ij}}}\right)\end{aligned}}}">

<mtr>

<mtd>

</mtd>

<mtd>

</mrow>

</munder>

<msub>

</mrow>

</msub>

<msub>

</mrow>

</msub>

<msup>

</mrow>

</msup>

</mrow>

</munder>

<msub>

</mrow>

</msub>

<msub>

</mrow>

</msub>

<msup>

</mrow>

</msup>

</mrow>

</munder>

<msub>

</mrow>

</msub>

</mtd>

</mtr>

<mtr>

<mtd>

</mrow>

</munder>

<msub>

</mrow>

</msub>

<msub>

</mrow>

</msub>

<msup>

</mrow>

</msup>

</mrow>

</munder>

<msub>

</mrow>

</msub>

<msub>

</mrow>

</msub>

<msup>

</mrow>

</msup>

</mtd>

</mtr>

<mtr>

<mtd>

</mrow>

</munder>

<mrow>

<mrow>

<msub>

</mrow>

</msub>

<mrow>

<mrow>

<msup>

<mrow>

<mfrac>

<msub>

<msub>

</mrow>

</msub>

</mrow>

</msub>

<msub>

</mrow>

</msub>

</mfrac>

</mrow>

</mrow>

</mrow>

</msup>

<msup>

<mrow>

<mfrac>

<msub>

<msub>

</mrow>

</msub>

</mrow>

</msub>

<msub>

</mrow>

</msub>

</mfrac>

</mrow>

</mrow>

</mrow>

</msup>

</mrow>

</mrow>

<mfrac>

<mrow>

<msub>

</mrow>

</msub>

<msub>

</mrow>

</msub>

</mrow>

<mrow>

<msub>

</mrow>

</msub>

<msub>

</mrow>

</msub>

</mrow>

</mfrac>

</mrow>

</mrow>

</mtd>

</mtr>

</mtable>

</mrow>

</mstyle>

</mrow>

<annotation encoding="application/x-tex">{\displaystyle {\begin{aligned}V=&\sum _{bonds}k_{b}(b-b_{0})^{2}+\sum _{angles}k_{\theta }(\theta -\theta _{0})^{2}+\sum _{dihedrals}k_{\phi }[1+\cos(n\phi -\delta )]\\&+\sum _{impropers}k_{\omega }(\omega -\omega _{0})^{2}+\sum _{Urey-Bradley}k_{u}(u-u_{0})^{2}\\&+\sum _{nonbonded}\left(\epsilon _{ij}\left[\left({\frac {R_{min_{ij}}}{r_{ij}}}\right)^{12}-2\left({\frac {R_{min_{ij}}}{r_{ij}}}\right)^{6}\right]+{\frac {q_{i}q_{j}}{\epsilon _{r}r_{ij}}}\right)\end{aligned}}}</annotation>

</semantics>

</math></span><img src="./e49a2f98eb5fcde99dac42b1253b65c5b77d187a.svg" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -9.671ex; width:69.251ex; height:20.509ex;" alt="{\displaystyle {\begin{aligned}V=&\sum _{bonds}k_{b}(b-b_{0})^{2}+\sum _{angles}k_{\theta }(\theta -\theta _{0})^{2}+\sum _{dihedrals}k_{\phi }[1+\cos(n\phi -\delta )]\\&+\sum _{impropers}k_{\omega }(\omega -\omega _{0})^{2}+\sum _{Urey-Bradley}k_{u}(u-u_{0})^{2}\\&+\sum _{nonbonded}\left(\epsilon _{ij}\left[\left({\frac {R_{min_{ij}}}{r_{ij}}}\right)^{12}-2\left({\frac {R_{min_{ij}}}{r_{ij}}}\right)^{6}\right]+{\frac {q_{i}q_{j}}{\epsilon _{r}r_{ij}}}\right)\end{aligned}}}" loading="lazy"></span>

</p><p>The bond, angle, dihedral, and nonbonded terms are similar to those found in other force fields such as <a href="AMBER#Functional_form" title="AMBER">AMBER</a>. The CHARMM force field also includes an improper term accounting for out-of-plane bending (which applies to any set of four atoms that are not successively bonded), where <span class="mwe-math-element mwe-math-element-inline"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle k_{\omega }}">

<msub>

</mrow>

</msub>

</mstyle>

</mrow>

<annotation encoding="application/x-tex">{\displaystyle k_{\omega }}</annotation>

</semantics>

</math></span><img src="./3d1ef146956fb7163b684fbc1c56bd96ead53af5.svg" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.671ex; width:2.466ex; height:2.509ex;" alt="{\displaystyle k_{\omega }}" loading="lazy"></span> is the force constant and <span class="mwe-math-element mwe-math-element-inline"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle \omega -\omega _{0}}">

<msub>

</mrow>

</msub>

</mstyle>

</mrow>

<annotation encoding="application/x-tex">{\displaystyle \omega -\omega _{0}}</annotation>

</semantics>

</math></span><img src="./223fef5a200abaa5d2acd16f22105e0387c33aa2.svg" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.671ex; width:6.786ex; height:2.343ex;" alt="{\displaystyle \omega -\omega _{0}}" loading="lazy"></span> is the out-of-plane angle. The Urey-Bradley term is a cross-term that accounts for 1,3 nonbonded interactions not accounted for by the bond and angle terms; <span class="mwe-math-element mwe-math-element-inline"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle k_{u}}">

<msub>

</mrow>

</msub>

</mstyle>

</mrow>

<annotation encoding="application/x-tex">{\displaystyle k_{u}}</annotation>

</semantics>

</math></span><img src="./271c4576ad6b3835df4470ddcf9aca83b36545fe.svg" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.671ex; width:2.384ex; height:2.509ex;" alt="{\displaystyle k_{u}}" loading="lazy"></span> is the force constant and <span class="mwe-math-element mwe-math-element-inline"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle u}">

</mstyle>

</mrow>

<annotation encoding="application/x-tex">{\displaystyle u}</annotation>

</semantics>

</math></span><img src="./c3e6bb763d22c20916ed4f0bb6bd49d7470cffd8.svg" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -0.338ex; width:1.33ex; height:1.676ex;" alt="{\displaystyle u}" loading="lazy"></span> is the distance between the 1,3 atoms.

</p><p>For <a href="DNA" title="DNA">DNA</a>, <a href="RNA" title="RNA">RNA</a>, and <a href="Lipid" title="Lipid">lipids</a>, CHARMM27<sup id="cite_ref-MacKerell2001_11-0" class="reference"><a href="#cite_note-MacKerell2001-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> is used. Some force fields may be combined, for example CHARMM22 and CHARMM27 for the simulation of protein-DNA binding. Also, parameters for NAD+, sugars, fluorinated compounds, etc., may be downloaded. These force field version numbers refer to the CHARMM version where they first appeared, but may of course be used with subsequent versions of the CHARMM executable program. Likewise, these force fields may be used within other molecular dynamics programs that support them.

</p><p>In 2009, a general force field for drug-like molecules (CGenFF) was introduced. It "covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds".<sup id="cite_ref-Vanommeslaeghe_12-0" class="reference"><a href="#cite_note-Vanommeslaeghe-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> The general force field is designed to cover any combination of chemical groups. This inevitably comes with a decrease in accuracy for representing any particular subclass of molecules. Users are repeatedly warned in Mackerell's website not to use the CGenFF parameters for molecules for which specialized force fields already exist (as mentioned above for proteins, nucleic acids, etc.).

</p><p>CHARMM also includes polarizable force fields using two approaches. One is based on the fluctuating charge (FQ) model, also termed Charge Equilibration (CHEQ).<sup id="cite_ref-Patel2004a_13-0" class="reference"><a href="#cite_note-Patel2004a-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Patel2004b_14-0" class="reference"><a href="#cite_note-Patel2004b-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> The other is based on the <a href="Drude_particle" title="Drude particle">Drude</a> shell or dispersion oscillator model.<sup id="cite_ref-Lamoureux_15-0" class="reference"><a href="#cite_note-Lamoureux-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Lamoureux3_16-0" class="reference"><a href="#cite_note-Lamoureux3-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup>

</p><p>Parameters for all of these force fields may be downloaded from the Mackerell website for free.<sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup>

</p>

<div class="mw-heading mw-heading2"><h2 id="Molecular_dynamics_program">Molecular dynamics program</h2></div>

<p>The CHARMM program allows for generating and analysing a wide range of molecular simulations. The most basic kinds of simulation are minimizing a given structure and production runs of a molecular dynamics trajectory. More advanced features include <a href="Free_energy_perturbation" class="mw-redirect" title="Free energy perturbation">free energy perturbation</a> (FEP), quasi-harmonic entropy estimation, correlation analysis and combined quantum, and <a href="Quantum_mechanics" title="Quantum mechanics">quantum mechanics</a>–<a href="Molecular_mechanics" title="Molecular mechanics">molecular mechanics</a> (<a href="QM/MM" title="QM/MM">QM/MM</a>) methods.

</p><p>CHARMM is one of the oldest programs for molecular dynamics. It has accumulated many features, some of which are duplicated under several keywords with slight variants. This is an inevitable result of the many outlooks and groups working on CHARMM worldwide. The <a rel="nofollow" class="external text" href="https://web.archive.org/web/20070907000754/http://www.charmm.org/package/changelogs/c34log.shtml">changelog file</a>, and CHARMM's source code, are good places to look for the names and affiliations of the main developers. The involvement and coordination by <a href="Charles_L._Brooks_III" title="Charles L. Brooks III">Charles L. Brooks III</a>'s group at the <a href="University_of_Michigan" title="University of Michigan">University of Michigan</a> is salient.

</p>

<div class="mw-heading mw-heading2"><h2 id="Software_history">Software history</h2></div>

<p>Around 1969, there was considerable interest in developing potential energy functions for small molecules. CHARMM originated at <a href="Martin_Karplus" title="Martin Karplus">Martin Karplus</a>'s group at Harvard. Karplus and his then graduate student Bruce Gelin decided the time was ripe to develop a program that would make it possible to take a given amino acid sequence and a set of coordinates (e.g., from the X-ray structure) and to use this information to calculate the energy of the system as a function of the atomic positions. Karplus has acknowledged the importance of major inputs in the development of the (at the time nameless) program, including:

</p>

<ul><li>Schneior Lifson's group at the Weizmann Institute, especially from <a href="Arieh_Warshel" title="Arieh Warshel">Arieh Warshel</a> who went to Harvard and brought his consistent force field (<b>CFF</b>) program with him</li>

<li><a href="Harold_Scheraga" title="Harold Scheraga">Harold Scheraga</a>'s group at Cornell University</li>

<li>Awareness of <a href="Michael_Levitt_(biophysicist)" title="Michael Levitt (biophysicist)">Michael Levitt</a>'s pioneering energy calculations for proteins</li></ul>

<p>In the 1980s, finally a paper appeared and CHARMM made its public début. Gelin's program had by then been considerably restructured. For the publication, Bob Bruccoleri came up with the name HARMM (HARvard Macromolecular Mechanics), but it seemed inappropriate. So they added a C for Chemistry. Karplus said: "<i>I sometimes wonder if Bruccoleri's original suggestion would have served as a useful warning to inexperienced scientists working with the program.</i>"<sup id="cite_ref-Karplus2006_18-0" class="reference"><a href="#cite_note-Karplus2006-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup> CHARMM has continued to grow and the latest release of the executable program was made in 2015 as CHARMM40b2.

</p>

<div class="mw-heading mw-heading2"><h2 id="Running_CHARMM_under_Unix-Linux">Running CHARMM under Unix-Linux</h2></div>

<p>The general syntax for using the program is:

</p><p><code>charmm -i filename.inp -o filename.out</code>

</p>

<ul><li><code>charmm</code> – The name of the program (or script which runs the program) on the computer system being used.</li>

<li><code>filename.inp</code> – A text file which contains the CHARMM commands. It starts by loading the molecular topologies (top) and <a href="Force_field_(chemistry)" title="Force field (chemistry)">force field</a> (par). Then one loads the molecular structures' Cartesian coordinates (e.g. from PDB files). One can then modify the molecules (adding hydrogens, changing secondary structure). The calculation section can include energy minimization, dynamics production, and analysis tools such as motion and energy correlations.</li>

<li><code>filename.out</code> – The log file for the CHARMM run, containing echoed commands, and various amounts of command output. The output print level may be increased or decreased in general, and procedures such as minimization and dynamics have printout frequency specifications. The values for temperature, energy pressure, etc. are output at that frequency.</li></ul>

<div class="mw-heading mw-heading2"><h2 id="Volunteer_computing">Volunteer computing</h2></div>

<p><a href="Docking%40Home" title="Docking@Home">Docking@Home</a>, hosted by University of Delaware, one of the projects which use an <a href="Open-source_software" title="Open-source software">open-source</a> platform for the <a href="Distributed_computing" title="Distributed computing">distributed computing</a>, <a href="BOINC" class="mw-redirect" title="BOINC">BOINC</a>, used CHARMM to analyze the atomic details of protein-ligand interactions in terms of <a href="Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a> (MD) simulations and minimizations.

</p><p><a href="World_Community_Grid" title="World Community Grid">World Community Grid</a>, sponsored by IBM, ran a project named The Clean Energy Project<sup id="cite_ref-19" class="reference"><a href="#cite_note-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> which also used CHARMM in its first phase, which has been completed.

</p>

/* start https://en.wikipedia.org/ */

.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}

/* end https://en.wikipedia.org/ */

</style><div class="div-col" style="column-width: 30em;">

<ul><li><a href="AMBER" title="AMBER">AMBER</a></li>

<li><a href="Ascalaph_Designer" title="Ascalaph Designer">Ascalaph Designer</a></li>

<li><a href="GROMACS" title="GROMACS">GROMACS</a></li>

<li><a href="Comparison_of_force_field_implementations" class="mw-redirect" title="Comparison of force field implementations">Comparison of force field implementations</a></li>

<li><a href="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="MacroModel" title="MacroModel">MacroModel</a></li>

<li><a href="MDynaMix" title="MDynaMix">MDynaMix</a></li>

<li><a href="Yasara" class="mw-redirect" title="Yasara">Yasara</a></li></ul></div>

<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

/* start https://en.wikipedia.org/ */

.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}

/* end https://en.wikipedia.org/ */

</style><div class="reflist reflist-columns references-column-width reflist-columns-2">

/* start https://en.wikipedia.org/ */

.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("./mw/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("./mw/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("./mw/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("./mw/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}}

/* end https://en.wikipedia.org/ */

</style><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://www.academiccharmm.org/program/versions">"Versions - CHARMM"</a>. <i>CHARMM (Chemistry at HARvard Macromolecular Mechanics)</i>. Harvard University<span class="reference-accessdate">. Retrieved <span class="nowrap">2021-03-29</span></span>.</cite></span>

</li>

<li id="cite_note-OS+platforms-2"><span class="mw-cite-backlink">^ <a href="#cite_ref-OS+platforms_2-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-OS+platforms_2-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://www.academiccharmm.org/documentation/installation#Documentation">"Installation"</a>. <i>CHARMM (Chemistry at HARvard Macromolecular Mechanics)</i>. Harvard University. 2016<span class="reference-accessdate">. Retrieved <span class="nowrap">2021-03-29</span></span>.</cite></span>

</li>

<li id="cite_note-Brooks1983-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-Brooks1983_3-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFBrooksBruccoleriOlafsonStates1983" class="citation journal cs1">Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983). "CHARMM: A program for macromolecular energy, minimization, and dynamics calculations". <i>J. Comput. Chem</i>. <b>4</b> (2): <span class="nowrap">187–</span>217. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.540040211">10.1002/jcc.540040211</a>. <a href="S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:91559650">91559650</a>.</cite></span>

</li>

<li id="cite_note-4"><span class="mw-cite-backlink"><b><a href="#cite_ref-4">^</a></b></span> <span class="reference-text"><cite id="CITEREFMacKerellBrooksBrooksNilsson1998" class="citation encyclopaedia cs1">MacKerell, A.D. Jr.; Brooks, B.; Brooks, C. L. III; Nilsson, L.; Roux, B.; Won, Y.; Karplus, M. (1998). "CHARMM: The Energy Function and Its Parameterization with an Overview of the Program". In Schleyer, P.v.R.; et al. (eds.). <i>The Encyclopedia of Computational Chemistry</i>. Vol. 1. Chichester: John Wiley & Sons. pp. <span class="nowrap">271–</span>277.</cite></span>

</li>

<li id="cite_note-5"><span class="mw-cite-backlink"><b><a href="#cite_ref-5">^</a></b></span> <span class="reference-text"><cite id="CITEREFBrooksBrooksMackerellNilsson2009" class="citation journal cs1">Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (29 July 2009). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810661">"CHARMM: The biomolecular simulation program"</a>. <i>Journal of Computational Chemistry</i>. <b>30</b> (10): <span class="nowrap">1545–</span>1614. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.21287">10.1002/jcc.21287</a>. <a href="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/PMC2810661">2810661</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/19444816">19444816</a>.</cite></span>

</li>

<li id="cite_note-Reiher1985-6"><span class="mw-cite-backlink"><b><a href="#cite_ref-Reiher1985_6-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFReiher,_III_WH1985" class="citation thesis cs1">Reiher, III WH (1985). <i>Theoretical studies of hydrogen bonding</i> (Thesis). Harvard University.</cite></span>

</li>

<li id="cite_note-MacKerell1998-7"><span class="mw-cite-backlink">^ <a href="#cite_ref-MacKerell1998_7-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-MacKerell1998_7-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><cite id="CITEREFMacKerell_AD_Jr1998" class="citation journal cs1">MacKerell AD Jr; et al. (1998). "All-atom empirical potential for molecular modeling and dynamics studies of proteins". <i>J Phys Chem B</i>. <b>102</b> (18): <span class="nowrap">3586–</span>3616. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1021%2Fjp973084f">10.1021/jp973084f</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/24889800">24889800</a>.</cite></span>

</li>

<li id="cite_note-MacKerell2004a-8"><span class="mw-cite-backlink"><b><a href="#cite_ref-MacKerell2004a_8-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFMacKerellFeigBrooks_III2004" class="citation journal cs1">MacKerell AD Jr, Feig M, Brooks III CL (2004). "Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations". <i>J Comput Chem</i>. <b>25</b> (11): <span class="nowrap">1400–</span>1415. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.20065">10.1002/jcc.20065</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/15185334">15185334</a>. <a href="S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:11076418">11076418</a>.</cite></span>

</li>

<li id="cite_note-Brooks2006-9"><span class="mw-cite-backlink"><b><a href="#cite_ref-Brooks2006_9-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFBrooksChenIm2006" class="citation journal cs1">Brooks CL, Chen J, Im W (2006). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596729">"Balancing solvation and intramolecular interactions: toward a consistent generalized born force field (CMAP opt. for GBSW)"</a>. <i>J Am Chem Soc</i>. <b>128</b> (11): <span class="nowrap">3728–</span>3736. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1021%2Fja057216r">10.1021/ja057216r</a>. <a href="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/PMC2596729">2596729</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16536547">16536547</a>.</cite></span>

</li>

<li id="cite_note-10"><span class="mw-cite-backlink"><b><a href="#cite_ref-10">^</a></b></span> <span class="reference-text"><cite id="CITEREFVanommeslaegheMacKerell2015" class="citation journal cs1">Vanommeslaeghe, K.; MacKerell, A. D. (May 2015). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334745">"CHARMM additive and polarizable force fields for biophysics and computer-aided drug design"</a>. <i>Biochimica et Biophysica Acta (BBA) - General Subjects</i>. <b>1850</b> (5): <span class="nowrap">861–</span>871. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.bbagen.2014.08.004">10.1016/j.bbagen.2014.08.004</a>. <a href="ISSN_(identifier)" class="mw-redirect" title="ISSN (identifier)">ISSN</a> <a rel="nofollow" class="external text" href="https://search.worldcat.org/issn/0006-3002">0006-3002</a>. <a href="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/PMC4334745">4334745</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/25149274">25149274</a>.</cite></span>

</li>

<li id="cite_note-MacKerell2001-11"><span class="mw-cite-backlink"><b><a href="#cite_ref-MacKerell2001_11-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFMacKerellBanavaliFoloppe2001" class="citation journal cs1">MacKerell AD Jr, Banavali N, Foloppe N (2001). "Development and current status of the CHARMM force field for nucleic acids". <i>Biopolymers</i>. <b>56</b> (4): <span class="nowrap">257–</span>265. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1002%2F1097-0282%282000%2956%3A4%3C257%3A%3AAID-BIP10029%3E3.0.CO%3B2-W">10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/11754339">11754339</a>. <a href="S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:19502363">19502363</a>.</cite></span>

</li>

<li id="cite_note-Vanommeslaeghe-12"><span class="mw-cite-backlink"><b><a href="#cite_ref-Vanommeslaeghe_12-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFVanommeslaegheHatcherAcharyaKundu2009" class="citation journal cs1">Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr (2009). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888302">"CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields"</a>. <i>J Comput Chem</i>. <b>31</b> (4): <span class="nowrap">671–</span>90. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.21367">10.1002/jcc.21367</a>. <a href="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/PMC2888302">2888302</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/19575467">19575467</a>.</cite></span>

</li>

<li id="cite_note-Patel2004a-13"><span class="mw-cite-backlink"><b><a href="#cite_ref-Patel2004a_13-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFPatelBrooks2004" class="citation journal cs1">Patel S, Brooks CL 3rd (2004). "CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations". <i>J Comput Chem</i>. <b>25</b> (1): <span class="nowrap">1–</span>15. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.10355">10.1002/jcc.10355</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/14634989">14634989</a>. <a href="S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:39320318">39320318</a>.</cite></span>

</li>

<li id="cite_note-Patel2004b-14"><span class="mw-cite-backlink"><b><a href="#cite_ref-Patel2004b_14-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFPatelMackerellBrooks2004" class="citation journal cs1">Patel S, Mackerell AD Jr, Brooks CL 3rd (2004). <a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.20077">"CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model"</a>. <i>J Comput Chem</i>. <b>25</b> (12): <span class="nowrap">1504–</span>1514. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1002%2Fjcc.20077">10.1002/jcc.20077</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/15224394">15224394</a>. <a href="S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:16741310">16741310</a>.</cite></span>

</li>

<li id="cite_note-Lamoureux-15"><span class="mw-cite-backlink"><b><a href="#cite_ref-Lamoureux_15-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFLamoureuxRoux2003" class="citation journal cs1">Lamoureux G, Roux B (2003). <a rel="nofollow" class="external text" href="https://doi.org/10.1063%2F1.1589749">"Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm"</a>. <i>J Chem Phys</i>. <b>119</b> (6): <span class="nowrap">3025–</span>3039. <a href="Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2003JChPh.119.3025L">2003JChPh.119.3025L</a>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1063%2F1.1589749">10.1063/1.1589749</a></span>.</cite></span>

</li>

<li id="cite_note-Lamoureux3-16"><span class="mw-cite-backlink"><b><a href="#cite_ref-Lamoureux3_16-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFLamoureuxHarderVorobyovRoux2006" class="citation journal cs1">Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD (2006). "A polarizable model of water for molecular dynamics simulations of biomolecules". <i>Chem Phys Lett</i>. <b>418</b> (<span class="nowrap">1–</span>3): <span class="nowrap">245–</span>249. <a href="Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2006CPL...418..245L">2006CPL...418..245L</a>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.cplett.2005.10.135">10.1016/j.cplett.2005.10.135</a>.</cite></span>

</li>

<li id="cite_note-17"><span class="mw-cite-backlink"><b><a href="#cite_ref-17">^</a></b></span> <span class="reference-text"><a rel="nofollow" class="external text" href="http://mackerell.umaryland.edu/CHARMM_ff_params.html">Mackerell website</a></span>

</li>

<li id="cite_note-Karplus2006-18"><span class="mw-cite-backlink"><b><a href="#cite_ref-Karplus2006_18-0">^</a></b></span> <span class="reference-text"><cite id="CITEREFKarplus_M2006" class="citation journal cs1">Karplus M (2006). "Spinach on the ceiling: a theoretical chemist's return to biology". <i>Annu Rev Biophys Biomol Struct</i>. <b>35</b> (1): <span class="nowrap">1–</span>47. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1146%2Fannurev.biophys.33.110502.133350">10.1146/annurev.biophys.33.110502.133350</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16689626">16689626</a>.</cite></span>

</li>

<li id="cite_note-19"><span class="mw-cite-backlink"><b><a href="#cite_ref-19">^</a></b></span> <span class="reference-text"><a rel="nofollow" class="external text" href="http://www.worldcommunitygrid.org/projects_showcase/cep1/viewCep1Main.do">The Clean Energy Project</a></span>

</li>

</ol></div>

<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>

<ul><li><span class="official-website"><span class="url"><a rel="nofollow" class="external text" href="http://www.academiccharmm.org">Official website</a></span></span>, with <a rel="nofollow" class="external text" href="https://www.academiccharmm.org/documentation">documentation</a> and helpful <a rel="nofollow" class="external text" href="https://www.charmm.org//ubbthreads/ubbthreads.php?Cat=">discussion forums</a></li>

<li><span class="official-website"><span class="url"><a rel="nofollow" class="external text" href="http://accelrys.com/products/collaborative-science/biovia-discovery-studio/simulations.html">Official website</a></span></span>, BIOVIA</li>

<li><a rel="nofollow" class="external text" href="http://www.ch.embnet.org/MD_tutorial/">CHARMM tutorial</a>; <a rel="nofollow" class="external text" href="https://web.archive.org/web/20101005042034/http://www.ch.embnet.org/MD_tutorial/">Archived</a> 2010-10-05 at the <a href="Wayback_Machine" title="Wayback Machine">Wayback Machine</a></li>

<li><a rel="nofollow" class="external text" href="http://www.pharmacy.umaryland.edu/faculty/amackere/">MacKerell</a> website, hosts package of force field parameters for CHARMM</li>

<li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20121017144252/http://brooks.chem.lsa.umich.edu/">C.Brooks website</a></li>

<li><a rel="nofollow" class="external text" href="http://yuri.harvard.edu/">CHARMM page at Harvard</a></li>

<li><a rel="nofollow" class="external text" href="http://thallium.bsd.uchicago.edu/RouxLab/">Roux website</a>; <a rel="nofollow" class="external text" href="https://web.archive.org/web/20061012004711/http://thallium.bsd.uchicago.edu/RouxLab/">Archived</a> 2006-10-12 at the <a href="Wayback_Machine" title="Wayback Machine">Wayback Machine</a></li>

<li><a rel="nofollow" class="external text" href="https://www.lobos.nih.gov/cbs/">Bernard R. Brooks Group website</a></li>

<li><a rel="nofollow" class="external text" href="http://docking.cis.udel.edu/">Docking@Home</a></li>

<li><a rel="nofollow" class="external text" href="http://www.charmm-gui.org/">CHARMM-GUI project</a></li>

<li><a rel="nofollow" class="external text" href="http://www.charmming.org/">CHARMMing (CHARMM Interface and Graphics)</a>; <a rel="nofollow" class="external text" href="https://web.archive.org/web/20080820003831/http://www.charmming.org/">Archived</a> 2008-08-20 at the <a href="Wayback_Machine" title="Wayback Machine">Wayback Machine</a></li>

<li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20080515090156/http://www.charmmtutorial.org/">CHARMM Tutorial</a></li></ul>

/* start https://en.wikipedia.org/ */

.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output .hlist ul{margin:0;padding:0}.mw-parser-output .hlist dd,.mw-parser-output .hlist dt,.mw-parser-output .hlist li{margin:0;display:inline}.mw-parser-output .hlist.inline,.mw-parser-output .hlist.inline dl,.mw-parser-output .hlist.inline ol,.mw-parser-output .hlist.inline ul,.mw-parser-output .hlist dl dl,.mw-parser-output .hlist dl ol,.mw-parser-output .hlist dl ul,.mw-parser-output .hlist ol dl,.mw-parser-output .hlist ol ol,.mw-parser-output .hlist ol ul,.mw-parser-output .hlist ul dl,.mw-parser-output .hlist ul ol,.mw-parser-output .hlist ul ul{display:inline}.mw-parser-output .hlist .mw-empty-li{display:none}.mw-parser-output .hlist dt::after{content:": "}.mw-parser-output .hlist dd::after,.mw-parser-output .hlist li::after{content:" · ";font-weight:bold}.mw-parser-output .hlist dd:last-child::after,.mw-parser-output .hlist dt:last-child::after,.mw-parser-output .hlist li:last-child::after{content:none}.mw-parser-output .hlist dd dd:first-child::before,.mw-parser-output .hlist dd dt:first-child::before,.mw-parser-output .hlist dd li:first-child::before,.mw-parser-output .hlist dt dd:first-child::before,.mw-parser-output .hlist dt dt:first-child::before,.mw-parser-output .hlist dt li:first-child::before,.mw-parser-output .hlist li dd:first-child::before,.mw-parser-output .hlist li dt:first-child::before,.mw-parser-output .hlist li li:first-child::before{content:" (";font-weight:normal}.mw-parser-output .hlist dd dd:last-child::after,.mw-parser-output .hlist dd dt:last-child::after,.mw-parser-output .hlist dd li:last-child::after,.mw-parser-output .hlist dt dd:last-child::after,.mw-parser-output .hlist dt dt:last-child::after,.mw-parser-output .hlist dt li:last-child::after,.mw-parser-output .hlist li dd:last-child::after,.mw-parser-output .hlist li dt:last-child::after,.mw-parser-output .hlist li li:last-child::after{content:")";font-weight:normal}.mw-parser-output .hlist ol{counter-reset:listitem}.mw-parser-output .hlist ol>li{counter-increment:listitem}.mw-parser-output .hlist ol>li::before{content:" "counter(listitem)"\a0 "}.mw-parser-output .hlist dd ol>li:first-child::before,.mw-parser-output .hlist dt ol>li:first-child::before,.mw-parser-output .hlist li ol>li:first-child::before{content:" ("counter(listitem)"\a0 "}

/* end https://en.wikipedia.org/ */

</style><style data-mw-deduplicate="TemplateStyles:r1236075235">

/* start https://en.wikipedia.org/ */

.mw-parser-output .navbox{box-sizing:border-box;border:1px solid #a2a9b1;width:100%;clear:both;font-size:88%;text-align:center;padding:1px;margin:1em auto 0}.mw-parser-output .navbox .navbox{margin-top:0}.mw-parser-output .navbox+.navbox,.mw-parser-output .navbox+.navbox-styles+.navbox{margin-top:-1px}.mw-parser-output .navbox-inner,.mw-parser-output .navbox-subgroup{width:100%}.mw-parser-output .navbox-group,.mw-parser-output .navbox-title,.mw-parser-output .navbox-abovebelow{padding:0.25em 1em;line-height:1.5em;text-align:center}.mw-parser-output .navbox-group{white-space:nowrap;text-align:right}.mw-parser-output .navbox,.mw-parser-output .navbox-subgroup{background-color:#fdfdfd}.mw-parser-output .navbox-list{line-height:1.5em;border-color:#fdfdfd}.mw-parser-output .navbox-list-with-group{text-align:left;border-left-width:2px;border-left-style:solid}.mw-parser-output tr+tr>.navbox-abovebelow,.mw-parser-output tr+tr>.navbox-group,.mw-parser-output tr+tr>.navbox-image,.mw-parser-output tr+tr>.navbox-list{border-top:2px solid #fdfdfd}.mw-parser-output .navbox-title{background-color:#ccf}.mw-parser-output .navbox-abovebelow,.mw-parser-output .navbox-group,.mw-parser-output .navbox-subgroup .navbox-title{background-color:#ddf}.mw-parser-output .navbox-subgroup .navbox-group,.mw-parser-output .navbox-subgroup .navbox-abovebelow{background-color:#e6e6ff}.mw-parser-output .navbox-even{background-color:#f7f7f7}.mw-parser-output .navbox-odd{background-color:transparent}.mw-parser-output .navbox .hlist td dl,.mw-parser-output .navbox .hlist td ol,.mw-parser-output .navbox .hlist td ul,.mw-parser-output .navbox td.hlist dl,.mw-parser-output .navbox td.hlist ol,.mw-parser-output .navbox td.hlist ul{padding:0.125em 0}.mw-parser-output .navbox .navbar{display:block;font-size:100%}.mw-parser-output .navbox-title .navbar{float:left;text-align:left;margin-right:0.5em}body.skin--responsive .mw-parser-output .navbox-image img{max-width:none!important}@media print{body.ns-0 .mw-parser-output .navbox{display:none!important}}

/* end https://en.wikipedia.org/ */

</style></div><div role="navigation" class="navbox" aria-labelledby="Computational_chemistry_software280" style="padding:3px"><table class="nowraplinks mw-collapsible autocollapse navbox-inner" style="border-spacing:0;background:transparent;color:inherit"><tbody><tr><th scope="col" class="navbox-title" colspan="2"><style data-mw-deduplicate="TemplateStyles:r1239400231">

/* start https://en.wikipedia.org/ */

.mw-parser-output .navbar{display:inline;font-size:88%;font-weight:normal}.mw-parser-output .navbar-collapse{float:left;text-align:left}.mw-parser-output .navbar-boxtext{word-spacing:0}.mw-parser-output .navbar ul{display:inline-block;white-space:nowrap;line-height:inherit}.mw-parser-output .navbar-brackets::before{margin-right:-0.125em;content:"[ "}.mw-parser-output .navbar-brackets::after{margin-left:-0.125em;content:" ]"}.mw-parser-output .navbar li{word-spacing:-0.125em}.mw-parser-output .navbar a>span,.mw-parser-output .navbar a>abbr{text-decoration:inherit}.mw-parser-output .navbar-mini abbr{font-variant:small-caps;border-bottom:none;text-decoration:none;cursor:inherit}.mw-parser-output .navbar-ct-full{font-size:114%;margin:0 7em}.mw-parser-output .navbar-ct-mini{font-size:114%;margin:0 4em}html.skin-theme-clientpref-night .mw-parser-output .navbar li a abbr{color:var(--color-base)!important}@media(prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .navbar li a abbr{color:var(--color-base)!important}}@media print{.mw-parser-output .navbar{display:none!important}}

/* end https://en.wikipedia.org/ */

</style><div id="Computational_chemistry_software280" style="font-size:114%;margin:0 4em"><a href="Computational_chemistry" title="Computational chemistry">Computational chemistry</a> software</div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Cheminformatics" title="Cheminformatics">Cheminformatics</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Free_software" title="Free software">Free software</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="Bioclipse" title="Bioclipse">Bioclipse</a></li>

<li><a href="Blue_Obelisk" title="Blue Obelisk">Blue Obelisk</a></li>

<li><a href="Chemistry_Development_Kit" title="Chemistry Development Kit">Chemistry Development Kit</a></li>

<li><a href="JOELib" title="JOELib">JOELib</a></li>

<li><a href="OELib" title="OELib">OELib</a></li>

<li><a href="Open_Babel" title="Open Babel">Open Babel</a></li>

<li><a href="RDKit" title="RDKit">RDKit</a></li></ul>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Proprietary_software" title="Proprietary software">Proprietary</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="AlvaDesc" title="AlvaDesc">AlvaDesc</a></li>

<li><a href="Schr%C3%B6dinger_(company)" class="mw-redirect" title="Schrödinger (company)">Canvas</a></li>

<li><a href="Chemicalize" title="Chemicalize">Chemicalize</a></li>

<li><a href="Discovery_Studio" title="Discovery Studio">Discovery Studio</a></li>

<li><a href="OpenEye_Scientific_Software" title="OpenEye Scientific Software"> OEChem TK</a></li></ul>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Chemical_kinetics" title="Chemical kinetics">Chemical kinetics</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Free software</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">

<li><a href="Cantera_(software)" title="Cantera (software)">Cantera</a></li>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Proprietary</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="Autochem" title="Autochem">Autochem</a></li>

<li><a href="Chemical_WorkBench" title="Chemical WorkBench">Chemical WorkBench</a></li>

<li><a href="CHEMKIN" title="CHEMKIN">CHEMKIN</a></li>

<li><a href="COSILAB" title="COSILAB">COSILAB</a></li>

<li><a href="DelPhi_(software)" class="mw-redirect" title="DelPhi (software)">DelPhi</a></li>

<li><a href="Khimera" title="Khimera">Khimera</a></li></ul>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Molecular_modelling" title="Molecular modelling">Molecular modelling</a> <br> and <br> <a href="Visualization_(graphics)" title="Visualization (graphics)">visualization</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="List_of_molecular_graphics_systems" title="List of molecular graphics systems">List of molecular graphics systems</a>

</div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Free software</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="Ascalaph_Designer" title="Ascalaph Designer">Ascalaph Designer</a></li>

<li><a href="Avogadro_(software)" title="Avogadro (software)">Avogadro</a></li>

<li><a href="Biskit" title="Biskit">Biskit</a></li>

<li><a href="Gabedit" title="Gabedit">Gabedit</a></li>

<li><a href="Ghemical" title="Ghemical">Ghemical</a></li>

<li><a href="Molekel" title="Molekel">Molekel</a></li>

<li><a href="PyMOL" title="PyMOL">PyMOL</a></li>

<li><a href="QuteMol" title="QuteMol">QuteMol</a></li>

<li><a href="RasMol" title="RasMol">RasMol</a></li></ul>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Proprietary</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="Abalone_(molecular_mechanics)" title="Abalone (molecular mechanics)">Abalone</a></li>

<li><a href="ACD/ChemSketch" title="ACD/ChemSketch">ACD/ChemSketch</a></li>

<li><a href="Atomistix_ToolKit" title="Atomistix ToolKit">Atomistix ToolKit</a></li>

<li><a href="ChemDraw" title="ChemDraw">ChemDraw</a></li>

<li><a href="ChemWindow" title="ChemWindow">ChemWindow</a></li>

<li><a href="EzMol" title="EzMol">EzMol</a></li>

<li><a href="Gaussian_(software)" title="Gaussian (software)">Gaussian</a></li>

<li><a href="Schr%C3%B6dinger_(company)" class="mw-redirect" title="Schrödinger (company)">Maestro</a></li>

<li><a href="MarvinSketch" class="mw-redirect" title="MarvinSketch">MarvinSketch</a></li>

<li><a href="MarvinView" class="mw-redirect" title="MarvinView">MarvinView</a></li>

<li><a href="MODELLER" title="MODELLER">MODELLER</a></li>

<li><a href="Molecular_Operating_Environment" title="Molecular Operating Environment">Molecular Operating Environment</a></li>

<li><a href="SAMSON" title="SAMSON">SAMSON</a></li>

<li><a href="Spartan_(chemistry_software)" title="Spartan (chemistry software)">Spartan</a></li>

<li><a href="UCSF_Chimera" title="UCSF Chimera">UCSF Chimera</a></li>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Docking_(molecular)" title="Docking (molecular)">Molecular docking</a></th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="List_of_protein-ligand_docking_software" title="List of protein-ligand docking software">List of protein-ligand docking software</a>

</div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Free_software" title="Free software">Free software</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="AutoDock" title="AutoDock">AutoDock</a></li>

<li><a href="AutoDock_Vina" class="mw-redirect" title="AutoDock Vina">AutoDock Vina</a></li>

<li><a href="FlexAID" title="FlexAID">FlexAID</a></li>

<li><a href="RDock" title="RDock">rDock</a></li></ul>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Proprietary_software" title="Proprietary software">Proprietary</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="Glide_(docking)" title="Glide (docking)">Glide</a></li>

<li><a href="LeDock" title="LeDock">LeDock</a></li>

<li><a href="Molecular_Operating_Environment" title="Molecular Operating Environment">Molecular Operating Environment</a></li>

<li><a href="OpenEye_Scientific_Software" title="OpenEye Scientific Software"> OEDocking</a></li></ul>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Molecular_dynamics" title="Molecular dynamics">Molecular dynamics</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Free_software" title="Free software">Free software</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">

<li><a href="GROMACS" title="GROMACS">GROMACS</a></li>

<li><a href="LAMMPS" title="LAMMPS">LAMMPS</a></li>

<li><a href="OpenMM" title="OpenMM">OpenMM</a></li>

<li><a href="PLUMED" title="PLUMED">PLUMED</a></li></ul>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Proprietary_software" title="Proprietary software">Proprietary</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="Abalone_(molecular_mechanics)" title="Abalone (molecular mechanics)">Abalone</a></li>

<li><a href="AMBER" title="AMBER">AMBER</a></li>

<li><a href="Desmond_(software)" title="Desmond (software)">Desmond</a></li>

<li><a href="GROMOS" title="GROMOS">GROMOS</a></li>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Quantum_chemistry" title="Quantum chemistry">Quantum chemistry</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="List_of_quantum_chemistry_and_solid-state_physics_software" title="List of quantum chemistry and solid-state physics software">List of quantum chemistry and solid-state physics software</a>

</div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Free software</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="ABINIT" title="ABINIT">ABINIT</a></li>

<li><a href="ACES_(computational_chemistry)" title="ACES (computational chemistry)">ACES</a> (CFOUR)</li>

<li><a href="AIMAll" title="AIMAll">AIMAll</a></li>

<li><a href="BigDFT" title="BigDFT">BigDFT</a></li>

<li><a href="COLUMBUS" title="COLUMBUS">COLUMBUS</a></li>

<li><a href="CONQUEST" title="CONQUEST">CONQUEST</a></li>

<li><a href="Dalton_(program)" title="Dalton (program)">Dalton</a></li>

<li><a href="Dirac_(software)" title="Dirac (software)">DIRAC</a></li>

<li><a href="FLEUR" title="FLEUR">FLEUR</a></li>

<li><a href="FreeON" title="FreeON">FreeON</a></li>

<li><a href="MADNESS" title="MADNESS">MADNESS</a></li>

<li><a href="MOPAC" title="MOPAC">MOPAC</a></li>

<li><a href="NWChem" title="NWChem">NWChem</a></li>

<li><a href="Octopus_(software)" title="Octopus (software)">Octopus</a></li>

<li><a href="MOLCAS" title="MOLCAS">OpenMolcas</a></li>

<li><a href="PARSEC" title="PARSEC">PARSEC</a></li>

<li>PyQuante</li>

<li><a href="PySCF" title="PySCF">PySCF</a></li>

<li><a href="Quantum_ESPRESSO" title="Quantum ESPRESSO">Quantum ESPRESSO</a> (PWscf)</li>

<li><a href="SIESTA_(computer_program)" title="SIESTA (computer program)">SIESTA</a></li>

<li><a href="YAMBO_code" title="YAMBO code">YAMBO code</a></li></ul>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Proprietary</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">

<li><a href="AMPAC" title="AMPAC">AMPAC</a></li>

<li><a href="CADPAC" title="CADPAC">CADPAC</a></li>

<li><a href="CASINO" title="CASINO">CASINO</a></li>

<li><a href="CASTEP" title="CASTEP">CASTEP</a></li>

<li><a href="Valence_bond_programs" title="Valence bond programs">CRUNCH</a></li>

<li><a href="CRYSTAL_(software)" title="CRYSTAL (software)">CRYSTAL</a></li>

<li><a href="Firefly_(computer_program)" title="Firefly (computer program)">Firefly</a></li>

<li><a href="GAMESS_(UK)" title="GAMESS (UK)">GAMESS (UK)</a></li>

<li><a href="GAMESS_(US)" title="GAMESS (US)">GAMESS (US)</a></li>

<li><a href="Gaussian_(software)" title="Gaussian (software)">Gaussian</a></li>

<li><a href="Jaguar_(software)" title="Jaguar (software)">Jaguar</a></li>

<li><a href="MOLCAS" title="MOLCAS">MOLCAS</a></li>

<li><a href="MOLPRO" title="MOLPRO">MOLPRO</a></li>

<li><a href="ONETEP" title="ONETEP">ONETEP</a></li>

<li><a href="OpenAtom" title="OpenAtom">OpenAtom</a></li>

<li><a href="PLATO_(computational_chemistry)" title="PLATO (computational chemistry)">PLATO</a></li>

<li><a href="Quantemol" title="Quantemol">Quantemol</a></li>

<li><a href="Scigress" title="Scigress">Scigress</a></li>

<li><a href="Spartan_(chemistry_software)" title="Spartan (chemistry software)">Spartan</a></li>

<li><a href="TeraChem" title="TeraChem">TeraChem</a></li>

<li><a href="TURBOMOLE" title="TURBOMOLE">TURBOMOLE</a></li>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Skeletal_structure" class="mw-redirect" title="Skeletal structure">Skeletal structure</a> drawing</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Free software</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="JChemPaint" title="JChemPaint">JChemPaint</a></li>

<li><a href="Molsketch" class="mw-redirect" title="Molsketch">Molsketch</a></li>

<li><a href="XDrawChem" title="XDrawChem">XDrawChem</a></li></ul>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Proprietary</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="ACD/ChemSketch" title="ACD/ChemSketch">ACD/ChemSketch</a></li>

<li><a href="ISIS/Draw" title="ISIS/Draw">BIOVIA Draw</a></li>

<li>ChemDoodle</li>

<li><a href="ChemDraw" title="ChemDraw">ChemDraw</a></li>

<li><a href="ChemWindow" title="ChemWindow">ChemWindow</a></li>

<li><a href="JME_Molecule_Editor" title="JME Molecule Editor">JME Molecule Editor</a></li>

<li><a href="MarvinSketch" class="mw-redirect" title="MarvinSketch">MarvinSketch</a></li>

<li><a href="OpenEye_Scientific_Software" title="OpenEye Scientific Software"> PICTO</a></li></ul>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Others</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="Aqion" title="Aqion">Aqion</a></li>

<li><a href="Mercury_(crystallography)" title="Mercury (crystallography)">Mercury</a></li>

<li><a href="CrystalExplorer" title="CrystalExplorer">CrystalExplorer</a></li>

<li><a href="Internal_Coordinate_Mechanics" title="Internal Coordinate Mechanics">ICM</a> (ICM-Browser)</li>

<li><a href="Materials_Studio" title="Materials Studio">Materials Studio</a></li>

<li><a href="Molden" title="Molden">Molden</a></li>

<li><a href="OpenChrom" title="OpenChrom">OpenChrom</a></li>

<li>SASHIMI</li></ul>

</div></td></tr></tbody></table></div></div><div><div class="zim-footer">

This article is issued from <a class="external text" title="Last edited on 2025-07-19" href="https://en.wikipedia.org/wiki/?title=CHARMM&oldid=1301316556">Wikipedia</a>. The text is available under <a class="external text" href="https://creativecommons.org/licenses/by-sa/4.0/deed.en">Creative Commons Attribution-Share Alike 4.0</a> unless otherwise noted. Additional terms may apply for the media files.

</div>

</div></div>

</div>

</main>

</div>

</body></html>