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<li class="breadcrumb-item active"><span class="section-number">8.4.1. </span>CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="charmm-amber-compass-dreiding-and-opls-force-fields">
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<h1><span class="section-number">8.4.1. </span>CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields<a class="headerlink" href="#charmm-amber-compass-dreiding-and-opls-force-fields" title="Link to this heading"></a></h1>
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<p>A compact summary of the concepts, definitions, and properties of
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force fields with explicit bonded interactions (like the ones discussed
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in this HowTo) is given in <a class="reference internal" href="#typelabel2"><span class="std std-ref">(Gissinger)</span></a>.</p>
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<p>A force field has 2 parts: the formulas that define it and the
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coefficients used for a particular system. Here we only discuss
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formulas implemented in LAMMPS that correspond to formulas commonly used
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in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
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coefficients is done either from special sections in an input data file
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via the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command or in the input script with
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||
commands like <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> or <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> and so on. See the <a class="reference internal" href="Tools.html"><span class="doc">Tools</span></a> doc page for
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additional tools that can use CHARMM, AMBER, or Materials Studio
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generated files to assign force field coefficients and convert their
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output into LAMMPS input. LAMMPS input scripts can also be generated by
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<a class="reference external" href="https://charmm-gui.org/">charmm-gui.org</a>.</p>
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<section id="charmm-and-amber">
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<h2>CHARMM and AMBER<a class="headerlink" href="#charmm-and-amber" title="Link to this heading"></a></h2>
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<p>The <a class="reference external" href="https://mackerell.umaryland.edu/charmm_ff.shtml">CHARMM force field</a> <a class="reference internal" href="#howto-mackerell"><span class="std std-ref">(MacKerell)</span></a> and <a class="reference external" href="https://ambermd.org/AmberModels.php">AMBER force field</a> <a class="reference internal" href="#howto-cornell"><span class="std std-ref">(Cornell)</span></a>
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have potential energy function of the form</p>
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<div class="math notranslate nohighlight">
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\[\begin{split}V & = \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{
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\text{charmm} \\
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\text{charmmfsw}
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}} +\!\!\! \sum_{impropers} \!\!\!E_i \\[.6em]
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& \quad + \!\!\!\!\!\!\!\!\!\!\underbrace{~\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}_{\substack{
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\text{lj/charmm/coul/charmm} \\
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\text{lj/charmm/coul/charmm/implicit} \\
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\text{lj/charmm/coul/long} \\
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\text{lj/charmm/coul/msm} \\
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\text{lj/charmmfsw/coul/charmmfsh} \\
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\text{lj/charmmfsw/coul/long}
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}} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)}\end{split}\]</div>
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<p>The terms are computed by bond styles (relationship between two atoms),
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angle styles (between 3 atoms) , dihedral/improper styles (between 4
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atoms), pair styles (non-covalently bonded pair interactions) and
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special bonds. The CMAP term (see <a class="reference internal" href="fix_cmap.html"><span class="doc">fix cmap</span></a> command for
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details) corrects for pairs of dihedral angles (“Correction MAP”) to
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significantly improve the structural and dynamic properties of proteins
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in crystalline and solution environments <a class="reference internal" href="#howto-brooks"><span class="std std-ref">(Brooks)</span></a>. The AMBER force field does not include the CMAP term.</p>
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<p>The interaction styles listed below compute force field formulas that
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are consistent with common options in CHARMM or AMBER. See each
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command’s documentation for the formula it computes.</p>
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<ul class="simple">
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<li><p><a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style</span></a> harmonic</p></li>
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<li><p><a class="reference internal" href="angle_charmm.html"><span class="doc">angle_style</span></a> charmm</p></li>
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<li><p><a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral_style</span></a> charmmfsh</p></li>
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<li><p><a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral_style</span></a> charmm</p></li>
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<li><p><a class="reference internal" href="pair_charmm.html"><span class="doc">pair_style</span></a> lj/charmmfsw/coul/charmmfsh</p></li>
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<li><p><a class="reference internal" href="pair_charmm.html"><span class="doc">pair_style</span></a> lj/charmmfsw/coul/long</p></li>
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<li><p><a class="reference internal" href="pair_charmm.html"><span class="doc">pair_style</span></a> lj/charmm/coul/charmm</p></li>
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<li><p><a class="reference internal" href="pair_charmm.html"><span class="doc">pair_style</span></a> lj/charmm/coul/charmm/implicit</p></li>
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<li><p><a class="reference internal" href="pair_charmm.html"><span class="doc">pair_style</span></a> lj/charmm/coul/long</p></li>
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<li><p><a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> charmm</p></li>
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<li><p><a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> amber</p></li>
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</ul>
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<p>The pair styles compute Lennard Jones (LJ) and Coulombic interactions
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with additional switching or shifting functions that ramp the energy
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and/or force smoothly to zero between an inner <span class="math notranslate nohighlight">\((a)\)</span> and outer
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<span class="math notranslate nohighlight">\((b)\)</span> cutoff. The older styles with <em>charmm</em> (not <em>charmmfsw</em> or
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<em>charmmfsh</em>) in their name compute the LJ and Coulombic interactions
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with an energy switching function (esw) <span class="math notranslate nohighlight">\(S(r)\)</span> which ramps the energy
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smoothly to zero between the inner and outer cutoff. This can cause
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irregularities in pairwise forces (due to the discontinuous second
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derivative of energy at the boundaries of the switching region), which
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in some cases can result in complications in energy minimization and
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detectable artifacts in MD simulations.</p>
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<div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils">
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||
<div class="sd-row sd-row-cols-1 sd-row-cols-xs-1 sd-row-cols-sm-1 sd-row-cols-md-2 sd-row-cols-lg-2 docutils">
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<div class="sd-col sd-d-flex-column docutils">
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||
<div class="math notranslate nohighlight">
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||
\[\begin{split}LJ(r) &= 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
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\left(\frac{\sigma}{r}\right)^6 \right]\\[.6em]
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C(r) &= \frac{C q_i q_j}{ \epsilon r}\\[.6em]
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S(r) &= \frac{ \left(b^2 - r^2\right)^2 \left(b^2 + 2r^2 - 3{a^2}\right)}
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{ \left(b^2 - a^2\right)^3 }\\[.6em]
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E_{LJ}(r) &= \begin{cases}
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LJ(r), & r \leq a \\
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LJ(r) S(r), & a < r \leq b \\
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0, &r > b
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\end{cases} \\[.6em]
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E_{coul}(r) &= \begin{cases}
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C(r), & r \leq a \\
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C(r) S(r), & a < r \leq b \\
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0, & r > b
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\end{cases}\end{split}\]</div>
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||
</div>
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||
<div class="sd-col sd-d-flex-column docutils">
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||
<img alt="_images/howto_charmm_ELJ.png" class="align-center" src="_images/howto_charmm_ELJ.png" />
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||
</div>
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</div>
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</div>
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<p>The newer styles with <em>charmmfsw</em> or <em>charmmfsh</em> in their name replace
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energy switching with force switching (fsw) for LJ interactions and
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force shifting (fsh) functions for Coulombic interactions
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<a class="reference internal" href="#howto-steinbach"><span class="std std-ref">(Steinbach)</span></a></p>
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||
<div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils">
|
||
<div class="sd-row sd-row-cols-1 sd-row-cols-xs-1 sd-row-cols-sm-1 sd-row-cols-md-2 sd-row-cols-lg-2 docutils">
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<div class="sd-col sd-d-flex-column docutils">
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<div class="math notranslate nohighlight">
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\[\begin{split} E_{LJ}(r) = & \begin{cases}
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4 \epsilon \sigma^6 \left(\frac{\displaystyle\sigma
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^6-r^6}{\displaystyle r^{12}}-\frac{\displaystyle\sigma ^6}{\displaystyle a^6
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b^6}+\frac{\displaystyle 1}{\displaystyle a^3 b^3}\right) & r\leq a \\
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\frac{\displaystyle 4 \epsilon \sigma^6 \left(\sigma ^6
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\left(b^6-r^6\right)^2-b^3 r^6 \left(a^3+b^3\right)
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\left(b^3-r^3\right)^2\right)}{\displaystyle b^6 r^{12}
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\left(b^6-a^6\right)} & a<r \leq b\\
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0, & r>b
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\end{cases}\\[.6em]
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E_{coul}(r) & = \begin{cases}
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C(r) \frac{\displaystyle (b-r)^2}{\displaystyle r b^2}, & r \leq b \\
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0, & r > b
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\end{cases}\end{split}\]</div>
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</div>
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<div class="sd-col sd-d-flex-column docutils">
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<img alt="_images/howto_charmmfsw_ELJ.png" class="align-center" src="_images/howto_charmmfsw_ELJ.png" />
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</div>
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</div>
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</div>
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<p>These styles are used by LAMMPS input scripts generated by
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<a class="reference external" href="https://charmm-gui.org/">https://charmm-gui.org/</a> <a class="reference internal" href="#howto-brooks"><span class="std std-ref">(Brooks)</span></a>.</p>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>For CHARMM, newer <em>charmmfsw</em> or <em>charmmfsh</em> styles were released in
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March 2017. We recommend they be used instead of the older <em>charmm</em>
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styles. See discussion of the differences on the <a class="reference internal" href="pair_charmm.html"><span class="doc">pair charmm</span></a> and <a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral charmm</span></a> doc
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pages.</p>
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</div>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>The TIP3P water model is strongly recommended for use with the CHARMM
|
||
force field. In fact, <a class="reference external" href="https://matsci.org/t/using-spc-water-with-charmm-ff/24715">“using the SPC model with CHARMM parameters is
|
||
a bad idea”</a> and <a class="reference external" href="https://matsci.org/t/hybrid-pair-styles-for-charmm-and-tip4p-ew/32609">“to
|
||
enable TIP4P style water in CHARMM, you would have to write a new pair
|
||
style”</a>
|
||
. LAMMPS input scripts generated by Solution Builder on <a class="reference external" href="https://charmm-gui.org">https://charmm-gui.org</a>
|
||
use TIP3P molecules for solvation. Any other water model can and
|
||
probably will lead to false conclusions.</p>
|
||
</div>
|
||
</section>
|
||
<section id="compass">
|
||
<h2>COMPASS<a class="headerlink" href="#compass" title="Link to this heading"></a></h2>
|
||
<p>COMPASS is a general force field for atomistic simulation of common
|
||
organic molecules, inorganic small molecules, and polymers which was
|
||
developed using ab initio and empirical parameterization techniques
|
||
<a class="reference internal" href="#howto-sun"><span class="std std-ref">(Sun)</span></a>. See the <a class="reference internal" href="Tools.html"><span class="doc">Tools</span></a> page for the
|
||
msi2lmp tool for creating LAMMPS template input and data files from
|
||
BIOVIA’s Materials Studio files. Please note that the msi2lmp tool is
|
||
very old and largely unmaintained, so it does not support all features
|
||
of Materials Studio provided force field files, especially additions
|
||
during the last decade. You should watch the output carefully and
|
||
compare results, where possible. See <a class="reference internal" href="#howto-sun"><span class="std std-ref">(Sun)</span></a> for a
|
||
description of the COMPASS force field.</p>
|
||
<p>These interaction styles listed below compute force field formulas that
|
||
are consistent with the COMPASS force field. See each command’s
|
||
documentation for the formula it computes.</p>
|
||
<ul class="simple">
|
||
<li><p><a class="reference internal" href="bond_class2.html"><span class="doc">bond_style</span></a> class2</p></li>
|
||
<li><p><a class="reference internal" href="angle_class2.html"><span class="doc">angle_style</span></a> class2</p></li>
|
||
<li><p><a class="reference internal" href="dihedral_class2.html"><span class="doc">dihedral_style</span></a> class2</p></li>
|
||
<li><p><a class="reference internal" href="improper_class2.html"><span class="doc">improper_style</span></a> class2</p></li>
|
||
<li><p><a class="reference internal" href="pair_class2.html"><span class="doc">pair_style</span></a> lj/class2</p></li>
|
||
<li><p><a class="reference internal" href="pair_class2.html"><span class="doc">pair_style</span></a> lj/class2/coul/cut</p></li>
|
||
<li><p><a class="reference internal" href="pair_class2.html"><span class="doc">pair_style</span></a> lj/class2/coul/long</p></li>
|
||
<li><p><a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> lj/coul 0 0 1</p></li>
|
||
</ul>
|
||
</section>
|
||
<section id="dreiding">
|
||
<h2>DREIDING<a class="headerlink" href="#dreiding" title="Link to this heading"></a></h2>
|
||
<p>DREIDING is a generic force field developed by the <a class="reference external" href="http://www.wag.caltech.edu">Goddard group</a> at Caltech and is useful for predicting
|
||
structures and dynamics of organic, biological and main-group inorganic
|
||
molecules. The philosophy in DREIDING is to use general force constants
|
||
and geometry parameters based on simple hybridization considerations,
|
||
rather than individual force constants and geometric parameters that
|
||
depend on the particular combinations of atoms involved in the bond,
|
||
angle, or torsion terms. DREIDING has an <a class="reference internal" href="pair_hbond_dreiding.html"><span class="doc">explicit hydrogen bond
|
||
term</span></a> to describe interactions involving a
|
||
hydrogen atom on very electronegative atoms (N, O, F). Unlike CHARMM
|
||
or AMBER, the DREIDING force field has not been parameterized for
|
||
considering solvents (like water).</p>
|
||
<p>See <a class="reference internal" href="#howto-mayo"><span class="std std-ref">(Mayo)</span></a> for a description of the DREIDING force field</p>
|
||
<p>The interaction styles listed below compute force field formulas that
|
||
are consistent with the DREIDING force field. See each command’s
|
||
documentation for the formula it computes.</p>
|
||
<ul class="simple">
|
||
<li><p><a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style</span></a> harmonic</p></li>
|
||
<li><p><a class="reference internal" href="bond_morse.html"><span class="doc">bond_style</span></a> morse</p></li>
|
||
<li><p><a class="reference internal" href="angle_cosine_squared.html"><span class="doc">angle_style</span></a> cosine/squared</p></li>
|
||
<li><p><a class="reference internal" href="angle_harmonic.html"><span class="doc">angle_style</span></a> harmonic</p></li>
|
||
<li><p><a class="reference internal" href="angle_cosine.html"><span class="doc">angle_style</span></a> cosine</p></li>
|
||
<li><p><a class="reference internal" href="angle_cosine_periodic.html"><span class="doc">angle_style</span></a> cosine/periodic</p></li>
|
||
<li><p><a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral_style</span></a> charmm</p></li>
|
||
<li><p><a class="reference internal" href="improper_umbrella.html"><span class="doc">improper_style</span></a> umbrella</p></li>
|
||
<li><p><a class="reference internal" href="pair_buck.html"><span class="doc">pair_style</span></a> buck</p></li>
|
||
<li><p><a class="reference internal" href="pair_buck.html"><span class="doc">pair_style</span></a> buck/coul/cut</p></li>
|
||
<li><p><a class="reference internal" href="pair_buck.html"><span class="doc">pair_style</span></a> buck/coul/long</p></li>
|
||
<li><p><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style</span></a> lj/cut</p></li>
|
||
<li><p><a class="reference internal" href="pair_lj_cut_coul.html"><span class="doc">pair_style</span></a> lj/cut/coul/cut</p></li>
|
||
<li><p><a class="reference internal" href="pair_lj_cut_coul.html"><span class="doc">pair_style</span></a> lj/cut/coul/long</p></li>
|
||
<li><p><a class="reference internal" href="pair_hbond_dreiding.html"><span class="doc">pair_style</span></a> hbond/dreiding/lj</p></li>
|
||
<li><p><a class="reference internal" href="pair_hbond_dreiding.html"><span class="doc">pair_style</span></a> hbond/dreiding/morse</p></li>
|
||
<li><p><a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> dreiding</p></li>
|
||
</ul>
|
||
</section>
|
||
<section id="opls">
|
||
<h2>OPLS<a class="headerlink" href="#opls" title="Link to this heading"></a></h2>
|
||
<p>OPLS (Optimized Potentials for Liquid Simulations) is a general force
|
||
field for atomistic simulation of organic molecules in solvent. It was
|
||
developed by the <a class="reference external" href="https://traken.chem.yale.edu/oplsaam.html">Jorgensen group</a> at Purdue University and
|
||
later at Yale University. Multiple versions of the OPLS parameters
|
||
exist for united atom representations (OPLS-UA) and for all-atom
|
||
representations (OPLS-AA).</p>
|
||
<p>This force field is based on atom types mapped to specific functional
|
||
groups in organic and biological molecules. Each atom includes a
|
||
static, partial atomic charge reflecting the oxidation state of the
|
||
element derived from its bonded neighbors <a class="reference internal" href="#howto-jorgensen"><span class="std std-ref">(Jorgensen)</span></a> and computed based on increments determined by the
|
||
atom type of the atoms bond to it.</p>
|
||
<p>The interaction styles listed below compute force field formulas that
|
||
are fully or in part consistent with the OPLS style force fields. See
|
||
each command’s documentation for the formula it computes. Some are only
|
||
compatible with a subset of OPLS interactions.</p>
|
||
<ul class="simple">
|
||
<li><p><a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style</span></a> harmonic</p></li>
|
||
<li><p><a class="reference internal" href="angle_harmonic.html"><span class="doc">angle_style</span></a> harmonic</p></li>
|
||
<li><p><a class="reference internal" href="dihedral_opls.html"><span class="doc">dihedral_style</span></a> opls</p></li>
|
||
<li><p><a class="reference internal" href="improper_cvff.html"><span class="doc">improper_style</span></a> cvff</p></li>
|
||
<li><p><a class="reference internal" href="improper_fourier.html"><span class="doc">improper_style</span></a> fourier</p></li>
|
||
<li><p><a class="reference internal" href="improper_harmonic.html"><span class="doc">improper_style</span></a> harmonic</p></li>
|
||
<li><p><a class="reference internal" href="pair_lj_cut_coul.html"><span class="doc">pair_style</span></a> lj/cut/coul/cut</p></li>
|
||
<li><p><a class="reference internal" href="pair_lj_cut_coul.html"><span class="doc">pair_style</span></a> lj/cut/coul/long</p></li>
|
||
<li><p><a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> geometric</p></li>
|
||
<li><p><a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> lj/coul 0.0 0.0 0.5</p></li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p id="typelabel2"><strong>(Gissinger)</strong> J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).</p>
|
||
<p id="howto-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998). J Phys Chem, 102, 3586 . <a class="reference external" href="https://doi.org/10.1021/jp973084f">https://doi.org/10.1021/jp973084f</a></p>
|
||
<p id="howto-cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman (1995). JACS 117, 5179-5197. <a class="reference external" href="https://doi.org/10.1021/ja00124a002">https://doi.org/10.1021/ja00124a002</a></p>
|
||
<p id="howto-steinbach"><strong>(Steinbach)</strong> Steinbach, Brooks (1994). J Comput Chem, 15, 667. <a class="reference external" href="https://doi.org/10.1002/jcc.540150702">https://doi.org/10.1002/jcc.540150702</a></p>
|
||
<p id="howto-brooks"><strong>(Brooks)</strong> Brooks, et al (2009). J Comput Chem, 30, 1545. <a class="reference external" href="https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287">https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287</a></p>
|
||
<p id="howto-sun"><strong>(Sun)</strong> Sun (1998). J. Phys. Chem. B, 102, 7338-7364. <a class="reference external" href="https://doi.org/10.1021/jp980939v">https://doi.org/10.1021/jp980939v</a></p>
|
||
<p id="howto-mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. <a class="reference external" href="https://doi.org/10.1021/j100389a010">https://doi.org/10.1021/j100389a010</a></p>
|
||
<p id="howto-jorgensen"><strong>(Jorgensen)</strong> Jorgensen, Tirado-Rives (1988). J Am Chem Soc, 110, 1657-1666. <a class="reference external" href="https://doi.org/10.1021/ja00214a001">https://doi.org/10.1021/ja00214a001</a></p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
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|
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