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<div class="section" id="fix-spring-command">
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<span id="index-0"></span><h1>fix spring command<a class="headerlink" href="#fix-spring-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID spring keyword values
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>spring = style name of this fix command</li>
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<li>keyword = <em>tether</em> or <em>couple</em></li>
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</ul>
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<pre class="literal-block">
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<em>tether</em> values = K x y z R0
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K = spring constant (force/distance units)
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x,y,z = point to which spring is tethered
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R0 = equilibrium distance from tether point (distance units)
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<em>couple</em> values = group-ID2 K x y z R0
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group-ID2 = 2nd group to couple to fix group with a spring
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K = spring constant (force/distance units)
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x,y,z = direction of spring
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R0 = equilibrium distance of spring (distance units)
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0
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fix pull ligand spring tether 50.0 0.0 0.0 0.0 5.0
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fix pull ligand spring tether 50.0 NULL NULL 2.0 3.0
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fix 5 bilayer1 spring couple bilayer2 100.0 NULL NULL 10.0 0.0
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fix longitudinal pore spring couple ion 100.0 NULL NULL -20.0 0.0
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fix radial pore spring couple ion 100.0 0.0 0.0 NULL 5.0
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Apply a spring force to a group of atoms or between two groups of
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atoms. This is useful for applying an umbrella force to a small
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molecule or lightly tethering a large group of atoms (e.g. all the
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solvent or a large molecule) to the center of the simulation box so
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that it doesn’t wander away over the course of a long simulation. It
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can also be used to hold the centers of mass of two groups of atoms at
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a given distance or orientation with respect to each other.</p>
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<p>The <em>tether</em> style attaches a spring between a fixed point <em>x,y,z</em> and
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the center of mass of the fix group of atoms. The equilibrium
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position of the spring is R0. At each timestep the distance R from
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the center of mass of the group of atoms to the tethering point is
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computed, taking account of wrap-around in a periodic simulation box.
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A restoring force of magnitude K (R - R0) Mi / M is applied to each
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atom in the group where <em>K</em> is the spring constant, Mi is the mass of
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the atom, and M is the total mass of all atoms in the group. Note
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that <em>K</em> thus represents the total force on the group of atoms, not a
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per-atom force.</p>
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<p>The <em>couple</em> style links two groups of atoms together. The first
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group is the fix group; the second is specified by group-ID2. The
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groups are coupled together by a spring that is at equilibrium when
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the two groups are displaced by a vector <em>x,y,z</em> with respect to each
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other and at a distance R0 from that displacement. Note that <em>x,y,z</em>
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is the equilibrium displacement of group-ID2 relative to the fix
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group. Thus (1,1,0) is a different spring than (-1,-1,0). When the
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relative positions and distance between the two groups are not in
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equilibrium, the same spring force described above is applied to atoms
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in each of the two groups.</p>
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<p>For both the <em>tether</em> and <em>couple</em> styles, any of the x,y,z values can
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be specified as NULL which means do not include that dimension in the
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distance calculation or force application.</p>
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<p>The first example above pulls the ligand towards the point (0,0,0).
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The second example holds the ligand near the surface of a sphere of
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radius 5 around the point (0,0,0). The third example holds the ligand
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a distance 3 away from the z=2 plane (on either side).</p>
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<p>The fourth example holds 2 bilayers a distance 10 apart in z. For the
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last two examples, imagine a pore (a slab of atoms with a cylindrical
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hole cut out) oriented with the pore axis along z, and an ion moving
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within the pore. The fifth example holds the ion a distance of -20
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below the z = 0 center plane of the pore (umbrella sampling). The
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last example holds the ion a distance 5 away from the pore axis
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(assuming the center-of-mass of the pore in x,y is the pore axis).</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The center of mass of a group of atoms is calculated in
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“unwrapped” coordinates using atom image flags, which means that the
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group can straddle a periodic boundary. See the <a class="reference internal" href="dump.html"><em>dump</em></a> doc
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page for a discussion of unwrapped coordinates. It also means that a
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spring connecting two groups or a group and the tether point can cross
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a periodic boundary and its length be calculated correctly. One
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exception is for rigid bodies, which should not be used with the fix
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spring command, if the rigid body will cross a periodic boundary.
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This is because image flags for rigid bodies are used in a different
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way, as explained on the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> doc page.</p>
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</div>
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</div>
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option is supported by this
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fix to add the energy stored in the spring to the system’s potential
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energy as part of <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>.</p>
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<p>This fix computes a global scalar which can be accessed by various
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<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar is the
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spring energy = 0.5 * K * r^2.</p>
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<p>This fix also computes global 4-vector which can be accessed by
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various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The first 3
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quantities in the vector are xyz components of the total force added
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to the group of atoms by the spring. In the case of the <em>couple</em>
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style, it is the force on the fix group (group-ID) or the negative of
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the force on the 2nd group (group-ID2). The 4th quantity in the
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vector is the magnitude of the force added by the spring, as a
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positive value if (r-R0) > 0 and a negative value if (r-R0) < 0. This
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sign convention can be useful when using the spring force to compute a
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potential of mean force (PMF).</p>
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<p>The scalar and vector values calculated by this fix are “extensive”.</p>
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<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
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the <a class="reference internal" href="run.html"><em>run</em></a> command.</p>
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<p>The forces due to this fix are imposed during an energy minimization,
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invoked by the <a class="reference internal" href="minimize.html"><em>minimize</em></a> command.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">If you want the spring energy to be included in the total
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potential energy of the system (the quantity being minimized), you
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MUST enable the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option for this
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fix.</p>
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</div>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<blockquote>
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<div>none</div></blockquote>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="fix_drag.html"><em>fix drag</em></a>, <a class="reference internal" href="fix_spring_self.html"><em>fix spring/self</em></a>,
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<a class="reference internal" href="fix_spring_rg.html"><em>fix spring/rg</em></a>, <a class="reference internal" href="fix_smd.html"><em>fix smd</em></a></p>
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<p><strong>Default:</strong> none</p>
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