Page MenuHomec4science
Files F98079207

fix_spring.html
No OneTemporary
Actions

File Metadata

Created
Thu, Jan 9, 13:58

fix_spring.html
View Options

<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>fix spring command &mdash; LAMMPS documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="Manual.html" class="icon icon-home"> LAMMPS
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
&nbsp;
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="Manual.html">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>fix spring command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Website</a>
<a href="Section_commands.html#comm">Commands</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="fix-spring-command">
<span id="index-0"></span><h1>fix spring command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">spring</span> <span class="n">keyword</span> <span class="n">values</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>spring = style name of this fix command</li>
<li>keyword = <em>tether</em> or <em>couple</em></li>
</ul>
<pre class="literal-block">
<em>tether</em> values = K x y z R0
K = spring constant (force/distance units)
x,y,z = point to which spring is tethered
R0 = equilibrium distance from tether point (distance units)
<em>couple</em> values = group-ID2 K x y z R0
group-ID2 = 2nd group to couple to fix group with a spring
K = spring constant (force/distance units)
x,y,z = direction of spring
R0 = equilibrium distance of spring (distance units)
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">pull</span> <span class="n">ligand</span> <span class="n">spring</span> <span class="n">tether</span> <span class="mf">50.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">fix</span> <span class="n">pull</span> <span class="n">ligand</span> <span class="n">spring</span> <span class="n">tether</span> <span class="mf">50.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">5.0</span>
<span class="n">fix</span> <span class="n">pull</span> <span class="n">ligand</span> <span class="n">spring</span> <span class="n">tether</span> <span class="mf">50.0</span> <span class="n">NULL</span> <span class="n">NULL</span> <span class="mf">2.0</span> <span class="mf">3.0</span>
<span class="n">fix</span> <span class="mi">5</span> <span class="n">bilayer1</span> <span class="n">spring</span> <span class="n">couple</span> <span class="n">bilayer2</span> <span class="mf">100.0</span> <span class="n">NULL</span> <span class="n">NULL</span> <span class="mf">10.0</span> <span class="mf">0.0</span>
<span class="n">fix</span> <span class="n">longitudinal</span> <span class="n">pore</span> <span class="n">spring</span> <span class="n">couple</span> <span class="n">ion</span> <span class="mf">100.0</span> <span class="n">NULL</span> <span class="n">NULL</span> <span class="o">-</span><span class="mf">20.0</span> <span class="mf">0.0</span>
<span class="n">fix</span> <span class="n">radial</span> <span class="n">pore</span> <span class="n">spring</span> <span class="n">couple</span> <span class="n">ion</span> <span class="mf">100.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">NULL</span> <span class="mf">5.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Apply a spring force to a group of atoms or between two groups of
atoms. This is useful for applying an umbrella force to a small
molecule or lightly tethering a large group of atoms (e.g. all the
solvent or a large molecule) to the center of the simulation box so
that it doesn&#8217;t wander away over the course of a long simulation. It
can also be used to hold the centers of mass of two groups of atoms at
a given distance or orientation with respect to each other.</p>
<p>The <em>tether</em> style attaches a spring between a fixed point <em>x,y,z</em> and
the center of mass of the fix group of atoms. The equilibrium
position of the spring is R0. At each timestep the distance R from
the center of mass of the group of atoms to the tethering point is
computed, taking account of wrap-around in a periodic simulation box.
A restoring force of magnitude K (R - R0) Mi / M is applied to each
atom in the group where <em>K</em> is the spring constant, Mi is the mass of
the atom, and M is the total mass of all atoms in the group. Note
that <em>K</em> thus represents the total force on the group of atoms, not a
per-atom force.</p>
<p>The <em>couple</em> style links two groups of atoms together. The first
group is the fix group; the second is specified by group-ID2. The
groups are coupled together by a spring that is at equilibrium when
the two groups are displaced by a vector <em>x,y,z</em> with respect to each
other and at a distance R0 from that displacement. Note that <em>x,y,z</em>
is the equilibrium displacement of group-ID2 relative to the fix
group. Thus (1,1,0) is a different spring than (-1,-1,0). When the
relative positions and distance between the two groups are not in
equilibrium, the same spring force described above is applied to atoms
in each of the two groups.</p>
<p>For both the <em>tether</em> and <em>couple</em> styles, any of the x,y,z values can
be specified as NULL which means do not include that dimension in the
distance calculation or force application.</p>
<p>The first example above pulls the ligand towards the point (0,0,0).
The second example holds the ligand near the surface of a sphere of
radius 5 around the point (0,0,0). The third example holds the ligand
a distance 3 away from the z=2 plane (on either side).</p>
<p>The fourth example holds 2 bilayers a distance 10 apart in z. For the
last two examples, imagine a pore (a slab of atoms with a cylindrical
hole cut out) oriented with the pore axis along z, and an ion moving
within the pore. The fifth example holds the ion a distance of -20
below the z = 0 center plane of the pore (umbrella sampling). The
last example holds the ion a distance 5 away from the pore axis
(assuming the center-of-mass of the pore in x,y is the pore axis).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The center of mass of a group of atoms is calculated in
&#8220;unwrapped&#8221; coordinates using atom image flags, which means that the
group can straddle a periodic boundary. See the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> doc
page for a discussion of unwrapped coordinates. It also means that a
spring connecting two groups or a group and the tether point can cross
a periodic boundary and its length be calculated correctly. One
exception is for rigid bodies, which should not be used with the fix
spring command, if the rigid body will cross a periodic boundary.
This is because image flags for rigid bodies are used in a different
way, as explained on the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> doc page.</p>
</div>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy stored in the spring to the system&#8217;s potential
energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
<p>This fix computes a global scalar which can be accessed by various
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar is the
spring energy = 0.5 * K * r^2.</p>
<p>This fix also computes global 4-vector which can be accessed by
various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The first 3
quantities in the vector are xyz components of the total force added
to the group of atoms by the spring. In the case of the <em>couple</em>
style, it is the force on the fix group (group-ID) or the negative of
the force on the 2nd group (group-ID2). The 4th quantity in the
vector is the magnitude of the force added by the spring, as a
positive value if (r-R0) &gt; 0 and a negative value if (r-R0) &lt; 0. This
sign convention can be useful when using the spring force to compute a
potential of mean force (PMF).</p>
<p>The scalar and vector values calculated by this fix are &#8220;extensive&#8221;.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
<p>The forces due to this fix are imposed during an energy minimization,
invoked by the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you want the spring energy to be included in the total
potential energy of the system (the quantity being minimized), you
MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option for this
fix.</p>
</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_drag.html"><span class="doc">fix drag</span></a>, <a class="reference internal" href="fix_spring_self.html"><span class="doc">fix spring/self</span></a>,
<a class="reference internal" href="fix_spring_rg.html"><span class="doc">fix spring/rg</span></a>, <a class="reference internal" href="fix_smd.html"><span class="doc">fix smd</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
</script>
</body>
</html>

Event Timeline

c4science · Help