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<li class="breadcrumb-item active"><span class="section-number">8.4.2. </span>AMOEBA and HIPPO 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="amoeba-and-hippo-force-fields">
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<h1><span class="section-number">8.4.2. </span>AMOEBA and HIPPO force fields<a class="headerlink" href="#amoeba-and-hippo-force-fields" title="Link to this heading"></a></h1>
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<p>The AMOEBA and HIPPO polarizable force fields were developed by Jay
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Ponder’s group at the U Washington at St Louis. The LAMMPS
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implementation is based on Fortran 90 code provided by the Ponder
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group in their <a class="reference external" href="https://dasher.wustl.edu/tinker/">Tinker MD software</a>.</p>
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<p>The current implementation (July 2022) of AMOEBA in LAMMPS matches the
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version discussed in <a class="reference internal" href="pair_amoeba.html#amoeba-ponder"><span class="std std-ref">(Ponder)</span></a>, <a class="reference internal" href="pair_amoeba.html#amoeba-ren"><span class="std std-ref">(Ren)</span></a>, and <a class="reference internal" href="pair_amoeba.html#amoeba-shi"><span class="std std-ref">(Shi)</span></a>. Likewise the current
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implementation of HIPPO in LAMMPS matches the version discussed in
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<a class="reference internal" href="pair_amoeba.html#amoeba-rackers"><span class="std std-ref">(Rackers)</span></a>.</p>
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<p>These force fields can be used when polarization effects are desired
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in simulations of water, organic molecules, and biomolecules including
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proteins, provided that parameterizations (Tinker PRM force field
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files) are available for the systems you are interested in. Files in
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the LAMMPS potentials directory with a “amoeba” or “hippo” suffix can
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be used. The Tinker distribution and website have additional force
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field files as well:
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<a class="reference external" href="https://github.com/TinkerTools/tinker/tree/release/params">https://github.com/TinkerTools/tinker/tree/release/params</a>.</p>
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<p>Note that currently, HIPPO can only be used for water systems, but
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HIPPO files for a variety of small organic and biomolecules are in
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preparation by the Ponder group. Those force field files will be
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included in the LAMMPS distribution when available.</p>
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<p>To use the AMOEBA or HIPPO force fields, a simulation must be 3d, and
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fully periodic or fully non-periodic, and use an orthogonal (not
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triclinic) simulation box.</p>
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<hr class="docutils" />
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<p>The AMOEBA and HIPPO force fields contain the following terms in their
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energy (U) computation. Further details for AMOEBA equations are in
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<a class="reference internal" href="pair_amoeba.html#amoeba-ponder"><span class="std std-ref">(Ponder)</span></a>, further details for the HIPPO
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equations are in <a class="reference internal" href="pair_amoeba.html#amoeba-rackers"><span class="std std-ref">(Rackers)</span></a>.</p>
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<div class="math notranslate nohighlight">
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\[\begin{split}U & = U_{intermolecular} + U_{intramolecular} \\
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U_{intermolecular} & = U_{hal} + U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer} \\
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U_{intramolecular} & = U_{bond} + U_{angle} + U_{torsion} + U_{oop} + U_{b\theta} + U_{UB} + U_{pitorsion} + U_{bitorsion}\end{split}\]</div>
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<p>For intermolecular terms, the AMOEBA force field includes only the
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<span class="math notranslate nohighlight">\(U_{hal}\)</span>, <span class="math notranslate nohighlight">\(U_{multipole}\)</span>, <span class="math notranslate nohighlight">\(U_{polar}\)</span> terms. The
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HIPPO force field includes all but the <span class="math notranslate nohighlight">\(U_{hal}\)</span> term. In
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LAMMPS, these are all computed by the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style amoeba or hippo</span></a> command. Note that the <span class="math notranslate nohighlight">\(U_{multipole}\)</span> and
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<span class="math notranslate nohighlight">\(U_{polar}\)</span> terms in this formula are not the same for the
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AMOEBA and HIPPO force fields.</p>
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<p>For intramolecular terms, the <span class="math notranslate nohighlight">\(U_{bond}\)</span>, <span class="math notranslate nohighlight">\(U_{angle}\)</span>,
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<span class="math notranslate nohighlight">\(U_{torsion}\)</span>, <span class="math notranslate nohighlight">\(U_{oop}\)</span> terms are computed by the
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<a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a> <a class="reference internal" href="angle_amoeba.html"><span class="doc">angle_style amoeba</span></a>, <a class="reference internal" href="dihedral_fourier.html"><span class="doc">dihedral_style fourier</span></a>, and
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<a class="reference internal" href="improper_amoeba.html"><span class="doc">improper_style amoeba</span></a> commands respectively.
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The <a class="reference internal" href="angle_amoeba.html"><span class="doc">angle_style amoeba</span></a> command includes the
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<span class="math notranslate nohighlight">\(U_{b\theta}\)</span> bond-angle cross term, and the <span class="math notranslate nohighlight">\(U_{UB}\)</span> term
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for a Urey-Bradley bond contribution between the I,K atoms in the IJK
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angle.</p>
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<p>The <span class="math notranslate nohighlight">\(U_{pitorsion}\)</span> term is computed by the <a class="reference internal" href="fix_amoeba_pitorsion.html"><span class="doc">fix
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amoeba/pitorsion</span></a> command. It computes 6-body
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interaction between a pair of bonded atoms which each have 2
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additional bond partners.</p>
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<p>The <span class="math notranslate nohighlight">\(U_{bitorsion}\)</span> term is computed by the <a class="reference internal" href="fix_amoeba_bitorsion.html"><span class="doc">fix
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amoeba/bitorsion</span></a> command. It computes 5-body
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interaction between two 4-body torsions (dihedrals) which overlap,
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having 3 atoms in common.</p>
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<p>These command doc pages have additional details on the terms they
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compute:</p>
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<ul class="simple">
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<li><p><a class="reference internal" href="pair_amoeba.html"><span class="doc">pair_style amoeba or hippo</span></a></p></li>
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<li><p><a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a></p></li>
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<li><p><a class="reference internal" href="angle_amoeba.html"><span class="doc">angle_style amoeba</span></a></p></li>
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<li><p><a class="reference internal" href="dihedral_fourier.html"><span class="doc">dihedral_style fourier</span></a></p></li>
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<li><p><a class="reference internal" href="improper_amoeba.html"><span class="doc">improper_style amoeba</span></a></p></li>
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<li><p><a class="reference internal" href="fix_amoeba_pitorsion.html"><span class="doc">fix amoeba/pitorsion</span></a></p></li>
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<li><p><a class="reference internal" href="fix_amoeba_bitorsion.html"><span class="doc">fix amoeba/bitorsion</span></a></p></li>
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</ul>
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<hr class="docutils" />
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<p>To use the AMOEBA or HIPPO force fields in LAMMPS, use commands like
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the following appropriately in your input script. The only change
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needed for AMOEBA vs HIPPO simulation is for the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> and <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> commands, as shown
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below. See examples/amoeba for example input scripts for both AMOEBA
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and HIPPO.</p>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">units</span><span class="w"> </span><span class="n">real</span><span class="w"> </span><span class="c"># required</span>
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<span class="k">atom_style</span><span class="w"> </span><span class="n">amoeba</span>
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<span class="k">bond_style</span><span class="w"> </span><span class="n">class2</span><span class="w"> </span><span class="c"># CLASS2 package</span>
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<span class="k">angle_style</span><span class="w"> </span><span class="n">amoeba</span>
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<span class="k">dihedral_style</span><span class="w"> </span><span class="n">fourier</span><span class="w"> </span><span class="c"># EXTRA-MOLECULE package</span>
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<span class="k">improper_style</span><span class="w"> </span><span class="n">amoeba</span>
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<span class="w"> </span><span class="c"># required per-atom data</span>
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<span class="k">fix </span><span class="nv nv-Identifier">amtype</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">property</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">i_amtype</span><span class="w"> </span><span class="n">ghost</span><span class="w"> </span><span class="n">yes</span>
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<span class="k">fix </span><span class="nv nv-Identifier">extra</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">property</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="o">&</span>
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<span class="w"> </span><span class="n">i_amgroup</span><span class="w"> </span><span class="n">i_ired</span><span class="w"> </span><span class="n">i_xaxis</span><span class="w"> </span><span class="n">i_yaxis</span><span class="w"> </span><span class="n">i_zaxis</span><span class="w"> </span><span class="n">d_pval</span><span class="w"> </span><span class="n">ghost</span><span class="w"> </span><span class="n">yes</span>
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<span class="k">fix </span><span class="nv nv-Identifier">polaxe</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">property</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">i_polaxe</span>
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<span class="k">fix </span><span class="nv nv-Identifier">pit</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">amoeba</span><span class="o">/</span><span class="n">pitorsion</span><span class="w"> </span><span class="c"># PiTorsion terms in FF</span>
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<span class="k">fix_modify </span><span class="nv nv-Identifier">pit</span><span class="w"> </span><span class="n">energy</span><span class="w"> </span><span class="n">yes</span>
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<span class="w"> </span><span class="c"># Bitorsion terms in FF</span>
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<span class="k">fix </span><span class="nv nv-Identifier">bit</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">amoeba</span><span class="o">/</span><span class="n">bitorsion</span><span class="w"> </span><span class="n">bitorsion.ubiquitin.data</span>
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<span class="k">fix_modify </span><span class="nv nv-Identifier">bit</span><span class="w"> </span><span class="n">energy</span><span class="w"> </span><span class="n">yes</span>
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<span class="k">read_data</span><span class="w"> </span><span class="n">data.ubiquitin</span><span class="w"> </span><span class="k">fix </span><span class="nv nv-Identifier">amtype</span><span class="w"> </span><span class="nv nv-Identifier">NULL</span><span class="w"> </span><span class="s">"Tinker Types"</span><span class="w"> </span><span class="o">&</span>
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||
<span class="w"> </span><span class="k">fix </span><span class="nv nv-Identifier">pit</span><span class="w"> </span><span class="s">"pitorsion types"</span><span class="w"> </span><span class="s">"PiTorsion Coeffs"</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="k">fix </span><span class="nv nv-Identifier">pit</span><span class="w"> </span><span class="nv nv-Identifier">pitorsions</span><span class="w"> </span><span class="n">PiTorsions</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="k">fix </span><span class="nv nv-Identifier">bit</span><span class="w"> </span><span class="nv nv-Identifier">bitorsions</span><span class="w"> </span><span class="n">BiTorsions</span>
|
||
|
||
<span class="k">pair_style</span><span class="w"> </span><span class="n">amoeba</span><span class="w"> </span><span class="c"># AMOEBA FF</span>
|
||
<span class="k">pair_coeff</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">amoeba_ubiquitin.prm</span><span class="w"> </span><span class="n">amoeba_ubiquitin.key</span>
|
||
|
||
<span class="k">pair_style</span><span class="w"> </span><span class="n">hippo</span><span class="w"> </span><span class="c"># HIPPO FF</span>
|
||
<span class="k">pair_coeff</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">hippo_water.prm</span><span class="w"> </span><span class="n">hippo_water.key</span>
|
||
|
||
<span class="k">special_bonds</span><span class="w"> </span><span class="n">lj</span><span class="o">/</span><span class="n">coul</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="m">0.5</span><span class="w"> </span><span class="n">one</span><span class="o">/</span><span class="n">five</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="c"># 1-5 neighbors</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The data file read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command should
|
||
be created by the tools/tinker/tinker2lmp.py conversion program
|
||
described below. It will create a section in the data file with the
|
||
header “Tinker Types”. A <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a>
|
||
command for the data must be specified before the read_data command.
|
||
In the example above the fix ID is <em>amtype</em>.</p>
|
||
<p>Similarly, if the system you are simulating defines AMOEBA/HIPPO
|
||
pitorsion or bitorsion interactions, there will be entries in the data
|
||
file for those interactions. They require a <a class="reference internal" href="fix_amoeba_pitorsion.html"><span class="doc">fix
|
||
amoeba/pitortion</span></a> and <a class="reference internal" href="fix_amoeba_bitorsion.html"><span class="doc">fix
|
||
amoeba/bitorsion</span></a> command be defined. In the
|
||
example above, the IDs for these two fixes are <em>pit</em> and <em>bit</em>.</p>
|
||
<p>Of course, if the system being modeled does not have one or more of
|
||
the following – bond, angle, dihedral, improper, pitorsion,
|
||
bitorsion interactions – then the corresponding style and fix
|
||
commands above do not need to be used. See the example scripts in
|
||
examples/amoeba for water systems as examples; they are simpler than
|
||
what is listed above.</p>
|
||
<p>The two <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> commands with IDs
|
||
(in the example above) <em>extra</em> and <em>polaxe</em> are also needed to define
|
||
internal per-atom quantities used by the AMOEBA and HIPPO force
|
||
fields.</p>
|
||
<p>The <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command used for either the AMOEBA
|
||
or HIPPO force field takes two arguments for Tinker force field files,
|
||
namely a PRM and KEY file. The keyfile can be specified as NULL and
|
||
default values for a various settings will be used. Note that these 2
|
||
files are meant to allow use of native Tinker files as-is. However
|
||
LAMMPS does not support all the options which can be included
|
||
in a Tinker PRM or KEY file. See specifics below.</p>
|
||
<p>A <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command with the <em>one/five</em>
|
||
option is required, since the AMOEBA/HIPPO force fields define
|
||
weighting factors for not only 1-2, 1-3, 1-4 interactions, but also
|
||
1-5 interactions. This command will trigger a per-atom list of 1-5
|
||
neighbors to be generated. The AMOEBA and HIPPO force fields define
|
||
their own custom weighting factors for all the 1-2, 1-3, 1-4, 1-5
|
||
terms which in the Tinker PRM and KEY files; they can be different for
|
||
different terms in the force field.</p>
|
||
<p>In addition to the list above, these command doc pages have additional
|
||
details:</p>
|
||
<ul class="simple">
|
||
<li><p><a class="reference internal" href="atom_style.html"><span class="doc">atom_style amoeba</span></a></p></li>
|
||
<li><p><a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a></p></li>
|
||
<li><p><a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a></p></li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p>Tinker PRM and KEY files</p>
|
||
<p>A Tinker PRM file is composed of sections, each of which has multiple
|
||
lines. This is the list of PRM sections LAMMPS knows how to parse and
|
||
use. Any other sections are skipped:</p>
|
||
<ul class="simple">
|
||
<li><p>Angle Bending Parameters</p></li>
|
||
<li><p>Atom Type Definitions</p></li>
|
||
<li><p>Atomic Multipole Parameters</p></li>
|
||
<li><p>Bond Stretching Parameters</p></li>
|
||
<li><p>Charge Penetration Parameters</p></li>
|
||
<li><p>Charge Transfer Parameters</p></li>
|
||
<li><p>Dipole Polarizability Parameters</p></li>
|
||
<li><p>Dispersion Parameters</p></li>
|
||
<li><p>Force Field Definition</p></li>
|
||
<li><p>Literature References</p></li>
|
||
<li><p>Out-of-Plane Bend Parameters</p></li>
|
||
<li><p>Pauli Repulsion Parameters</p></li>
|
||
<li><p>Pi-Torsion Parameters</p></li>
|
||
<li><p>Stretch-Bend Parameters</p></li>
|
||
<li><p>Torsion-Torsion Parameters</p></li>
|
||
<li><p>Torsional Parameters</p></li>
|
||
<li><p>Urey-Bradley Parameters</p></li>
|
||
<li><p>Van der Waals Pair Parameters</p></li>
|
||
<li><p>Van der Waals Parameters</p></li>
|
||
</ul>
|
||
<p>A Tinker KEY file is composed of lines, each of which has a keyword
|
||
followed by zero or more parameters. This is the list of keywords
|
||
LAMMPS knows how to parse and use in the same manner Tinker does. Any
|
||
other keywords are skipped. The value in parenthesis is the default
|
||
value for the keyword if it is not specified, or if the keyfile in the
|
||
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command is specified as NULL:</p>
|
||
<ul class="simple">
|
||
<li><p>a-axis (0.0)</p></li>
|
||
<li><p>b-axis (0.0)</p></li>
|
||
<li><p>c-axis (0.0)</p></li>
|
||
<li><p>ctrn-cutoff (6.0)</p></li>
|
||
<li><p>ctrn-taper (0.9 * ctrn-cutoff)</p></li>
|
||
<li><p>cutoff</p></li>
|
||
<li><p>delta-halgren (0.07)</p></li>
|
||
<li><p>dewald (no long-range dispersion unless specified)</p></li>
|
||
<li><p>dewald-alpha (0.4)</p></li>
|
||
<li><p>dewald-cutoff (7.0)</p></li>
|
||
<li><p>dispersion-cutoff (9.0)</p></li>
|
||
<li><p>dispersion-taper (9.0 * dispersion-cutoff)</p></li>
|
||
<li><p>dpme-grid</p></li>
|
||
<li><p>dpme-order (4)</p></li>
|
||
<li><p>ewald (no long-range electrostatics unless specified)</p></li>
|
||
<li><p>ewald-alpha (0.4)</p></li>
|
||
<li><p>ewald-cutoff (7.0)</p></li>
|
||
<li><p>gamma-halgren (0.12)</p></li>
|
||
<li><p>mpole-cutoff (9.0)</p></li>
|
||
<li><p>mpole-taper (0.65 * mpole-cutoff)</p></li>
|
||
<li><p>pcg-guess (enabled by default)</p></li>
|
||
<li><p>pcg-noguess (disable pcg-guess if specified)</p></li>
|
||
<li><p>pcg-noprecond (disable pcg-precond if specified)</p></li>
|
||
<li><p>pcg-peek (1.0)</p></li>
|
||
<li><p>pcg-precond (enabled by default)</p></li>
|
||
<li><p>pewald-alpha (0.4)</p></li>
|
||
<li><p>pme-grid</p></li>
|
||
<li><p>pme-order (5)</p></li>
|
||
<li><p>polar-eps (1.0e-6)</p></li>
|
||
<li><p>polar-iter (100)</p></li>
|
||
<li><p>polar-predict (no prediction operation unless specified)</p></li>
|
||
<li><p>ppme-order (5)</p></li>
|
||
<li><p>repulsion-cutoff (6.0)</p></li>
|
||
<li><p>repulsion-taper (0.9 * repulsion-cutoff)</p></li>
|
||
<li><p>taper</p></li>
|
||
<li><p>usolve-cutoff (4.5)</p></li>
|
||
<li><p>usolve-diag (2.0)</p></li>
|
||
<li><p>vdw-cutoff (9.0)</p></li>
|
||
<li><p>vdw-taper (0.9 * vdw-cutoff)</p></li>
|
||
</ul>
|
||
<hr class="docutils" />
|
||
<p>Tinker2lmp.py tool</p>
|
||
<p>This conversion tool is found in the tools/tinker directory.
|
||
As shown in examples/amoeba/README, these commands produce
|
||
the data files found in examples/amoeba, and also illustrate
|
||
all the options available to use with the tinker2lmp.py script:</p>
|
||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python<span class="w"> </span>tinker2lmp.py<span class="w"> </span>-xyz<span class="w"> </span>water_dimer.xyz<span class="w"> </span>-amoeba<span class="w"> </span>amoeba_water.prm<span class="w"> </span>-data<span class="w"> </span>data.water_dimer.amoeba<span class="w"> </span><span class="c1"># AMOEBA non-periodic system</span>
|
||
python<span class="w"> </span>tinker2lmp.py<span class="w"> </span>-xyz<span class="w"> </span>water_dimer.xyz<span class="w"> </span>-hippo<span class="w"> </span>hippo_water.prm<span class="w"> </span>-data<span class="w"> </span>data.water_dimer.hippo<span class="w"> </span><span class="c1"># HIPPO non-periodic system</span>
|
||
python<span class="w"> </span>tinker2lmp.py<span class="w"> </span>-xyz<span class="w"> </span>water_box.xyz<span class="w"> </span>-amoeba<span class="w"> </span>amoeba_water.prm<span class="w"> </span>-data<span class="w"> </span>data.water_box.amoeba<span class="w"> </span>-pbc<span class="w"> </span><span class="m">18</span>.643<span class="w"> </span><span class="m">18</span>.643<span class="w"> </span><span class="m">18</span>.643<span class="w"> </span><span class="c1"># AMOEBA periodic system</span>
|
||
python<span class="w"> </span>tinker2lmp.py<span class="w"> </span>-xyz<span class="w"> </span>water_box.xyz<span class="w"> </span>-hippo<span class="w"> </span>hippo_water.prm<span class="w"> </span>-data<span class="w"> </span>data.water_box.hippo<span class="w"> </span>-pbc<span class="w"> </span><span class="m">18</span>.643<span class="w"> </span><span class="m">18</span>.643<span class="w"> </span><span class="m">18</span>.643<span class="w"> </span><span class="c1"># HIPPO periodic system</span>
|
||
python<span class="w"> </span>tinker2lmp.py<span class="w"> </span>-xyz<span class="w"> </span>ubiquitin.xyz<span class="w"> </span>-amoeba<span class="w"> </span>amoeba_ubiquitin.prm<span class="w"> </span>-data<span class="w"> </span>data.ubiquitin.new<span class="w"> </span>-pbc<span class="w"> </span><span class="m">54</span>.99<span class="w"> </span><span class="m">41</span>.91<span class="w"> </span><span class="m">41</span>.91<span class="w"> </span>-bitorsion<span class="w"> </span>bitorsion.ubiquitin.data.new<span class="w"> </span><span class="c1"># system with bitorsions</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Switches and their arguments may be specified in any order.</p>
|
||
<p>The -xyz switch is required and specifies an input XYZ file as an
|
||
argument. The format of this file is an extended XYZ format defined
|
||
and used by Tinker for its input. Example *.xyz files are in the
|
||
examples/amoeba directory. The file lists the atoms in the system.
|
||
Each atom has the following information: Tinker species name (ignored
|
||
by LAMMPS), xyz coordinates, Tinker numeric type, and a list of atom
|
||
IDs the atom is bonded to.</p>
|
||
<p>Here is more information about the extended XYZ format defined and
|
||
used by Tinker, and links to programs that convert standard PDB files
|
||
to the extended XYZ format:</p>
|
||
<ul class="simple">
|
||
<li><p><a class="reference external" href="https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html">https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html</a></p></li>
|
||
<li><p><a class="reference external" href="https://github.com/emleddin/pdbxyz-xyzpdb">https://github.com/emleddin/pdbxyz-xyzpdb</a></p></li>
|
||
<li><p><a class="reference external" href="https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f">https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f</a></p></li>
|
||
</ul>
|
||
<p>The -amoeba or -hippo switch is required. It specifies an input
|
||
AMOEBA or HIPPO PRM force field file as an argument. This should be
|
||
the same file used by the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> command in
|
||
the input script.</p>
|
||
<p>The -data switch is required. It specifies an output file name for
|
||
the LAMMPS data file that will be produced.</p>
|
||
<p>For periodic systems, the -pbc switch is required. It specifies the
|
||
periodic box size for each dimension (x,y,z). For a Tinker simulation
|
||
these are specified in the KEY file.</p>
|
||
<p>The -bitorsion switch is only needed if the system contains Tinker
|
||
bitorsion interactions. The data for each type of bitorsion
|
||
interaction will be written to the specified file, and read by the
|
||
<a class="reference internal" href="fix_amoeba_bitorsion.html"><span class="doc">fix amoeba/bitorsion</span></a> command. The data
|
||
includes 2d arrays of values to which splines are fit, and thus is not
|
||
compatible with the LAMMPS data file format.</p>
|
||
<hr class="docutils" />
|
||
<p id="howto-ponder"><strong>(Ponder)</strong> Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).</p>
|
||
<p id="howto-rackers"><strong>(Rackers)</strong> Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).</p>
|
||
<p id="howto-ren"><strong>(Ren)</strong> Ren and Ponder, J Phys Chem B, 107, 5933 (2003).</p>
|
||
<p id="howto-shi"><strong>(Shi)</strong> Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.</p>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
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|
||
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|
||
<a href="Howto_bioFF.html" class="btn btn-neutral float-left" title="8.4.1. CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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||
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