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<div class="section" id="fix-smd-command">
<span id="index-0"></span><h1>fix smd command<a class="headerlink" href="#fix-smd-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID smd type values keyword values
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>smd = style name of this fix command</li>
<li>mode = <em>cvel</em> or <em>cfor</em> to select constant velocity or constant force SMD</li>
</ul>
<pre class="literal-block">
<em>cvel</em> values = K vel
K = spring constant (force/distance units)
vel = velocity of pulling (distance/time units)
<em>cfor</em> values = force
force = pulling force (force units)
</pre>
<ul class="simple">
<li>keyword = <em>tether</em> or <em>couple</em></li>
</ul>
<pre class="literal-block">
<em>tether</em> values = x y z R0
x,y,z = point to which spring is tethered
R0 = distance of end of spring from tether point (distance units)
<em>couple</em> values = group-ID2 x y z R0
group-ID2 = 2nd group to couple to fix group with a spring
x,y,z = direction of spring, automatically computed with 'auto'
R0 = distance of end of spring (distance units)
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0
fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>This fix implements several options of steered MD (SMD) as reviewed in
<span class="xref std std-ref">(Izrailev)</span>, which allows to induce conformational changes
in systems and to compute the potential of mean force (PMF) along the
assumed reaction coordinate <span class="xref std std-ref">(Park)</span> based on Jarzynski&#8217;s
equality <span class="xref std std-ref">(Jarzynski)</span>. This fix borrows a lot from <a class="reference internal" href="fix_spring.html"><em>fix spring</em></a> and <a class="reference internal" href="fix_setforce.html"><em>fix setforce</em></a>.</p>
<p>You can apply a moving spring force to a group of atoms (<em>tether</em>
style) or between two groups of atoms (<em>couple</em> style). The spring
can then be used in either constant velocity (<em>cvel</em>) mode or in
constant force (<em>cfor</em>) mode to induce transitions in your systems.
When running in <em>tether</em> style, you may need some way to fix some
other part of the system (e.g. via <a class="reference internal" href="fix_spring_self.html"><em>fix spring/self</em></a>)</p>
<p>The <em>tether</em> style attaches a spring between a point at a distance of
R0 away from a fixed point <em>x,y,z</em> and the center of mass of the fix
group of atoms. 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>In <em>cvel</em> mode the distance R is incremented or decremented
monotonously according to the pulling (or pushing) velocity.
In <em>cfor</em> mode a constant force is added and the actual distance
in direction of the spring is recorded.</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 in direction <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> only provides a direction and will be internally
normalized. But since it represents the <em>absolute</em> displacement of
group-ID2 relative to the fix group, (1,1,0) is a different spring
than (-1,-1,0). For each vector component, the displacement can be
described with the <em>auto</em> parameter. In this case the direction is
recomputed in every step, which can be useful for steering a local
process where the whole object undergoes some other change. 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>For constant velocity pulling (<em>cvel</em> mode), the running integral
over the pulling force in direction of the spring is recorded and
can then later be used to compute the potential of mean force (PMF)
by averaging over multiple independent trajectories along the same
pulling path.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<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>
<p>The fix stores the direction of the spring, current pulling target
distance and the running PMF to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.
See the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
fix.</p>
<p>This fix computes a vector list of 7 quantities, which can be accessed
by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The
quantities in the vector are in this order: the x-, y-, and
z-component of the pulling force, the total force in direction of the
pull, the equilibrium distance of the spring, the distance between the
two reference points, and finally the accumulated PMF (the sum of
pulling forces times displacement).</p>
<p>The force is the total force on 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 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"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="fix_drag.html"><em>fix drag</em></a>, <a class="reference internal" href="fix_spring.html"><em>fix spring</em></a>,
<a class="reference internal" href="fix_spring_self.html"><em>fix spring/self</em></a>,
<a class="reference internal" href="fix_spring_rg.html"><em>fix spring/rg</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="israilev"><strong>(Izrailev)</strong> Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.</p>
<p><strong>(Park)</strong>
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)</p>
<p><strong>(Jarzynski)</strong>
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)</p>
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