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<div class="section" id="fix-recenter-command">
<span id="index-0"></span><h1>fix recenter command<a class="headerlink" href="#fix-recenter-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 recenter x y z keyword value ...
</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>recenter = style name of this fix command</li>
<li>x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>shift</em> or <em>units</em></li>
</ul>
<pre class="literal-block">
<em>shift</em> value = group-ID
<HR>
<H3>fix recenter command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID recenter x y z keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>recenter = style name of this fix command
<LI>x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>shift</I> or <I>units</I>
<PRE> <I>shift</I> value = group-ID
group-ID = group of atoms whose coords are shifted
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>fraction</em>
</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 1 all recenter 0.0 0.5 0.0
<I>units</I> value = <I>box</I> or <I>lattice</I> or <I>fraction</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all recenter 0.0 0.5 0.0
fix 1 all recenter INIT INIT NULL
fix 1 all recenter INIT 0.0 0.0 units box
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Constrain the center-of-mass position of a group of atoms by adjusting
fix 1 all recenter INIT 0.0 0.0 units box
</PRE>
<P><B>Description:</B>
</P>
<P>Constrain the center-of-mass position of a group of atoms by adjusting
the coordinates of the atoms every timestep. This is simply a small
shift that does not alter the dynamics of the system or change the
relative coordinates of any pair of atoms in the group. This can be
used to insure the entire collection of atoms (or a portion of them)
do not drift during the simulation due to random perturbations
(e.g. <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> thermostatting).</p>
<p>Distance units for the x,y,z values are determined by the setting of
the <em>units</em> keyword, as discussed below. One or more x,y,z values can
(e.g. <A HREF = "fix_langevin.html">fix langevin</A> thermostatting).
</P>
<P>Distance units for the x,y,z values are determined by the setting of
the <I>units</I> keyword, as discussed below. One or more x,y,z values can
also be specified as NULL, which means exclude that dimension from
this operation. Or it can be specified as INIT which means to
constrain the center-of-mass to its initial value at the beginning of
the run.</p>
<p>The center-of-mass (COM) is computed for the group specified by the
the run.
</P>
<P>The center-of-mass (COM) is computed for the group specified by the
fix. If the current COM is different than the specified x,y,z, then a
group of atoms has their coordinates shifted by the difference. By
default the shifted group is also the group specified by the fix. A
different group can be shifted by using the <em>shift</em> keyword. For
different group can be shifted by using the <I>shift</I> keyword. For
example, the COM could be computed on a protein to keep it in the
center of the simulation box. But the entire system (protein + water)
could be shifted.</p>
<p>If the <em>units</em> keyword is set to <em>box</em>, then the distance units of
x,y,z are defined by the <a class="reference internal" href="units.html"><em>units</em></a> command - e.g. Angstroms
for <em>real</em> units. A <em>lattice</em> value means the distance units are in
lattice spacings. The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have been
previously used to define the lattice spacing. A <em>fraction</em> value
could be shifted.
</P>
<P>If the <I>units</I> keyword is set to <I>box</I>, then the distance units of
x,y,z are defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms
for <I>real</I> units. A <I>lattice</I> value means the distance units are in
lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have been
previously used to define the lattice spacing. A <I>fraction</I> value
means a fractional distance between the lo/hi box boundaries, e.g. 0.5
= middle of the box. The default is to use lattice units.</p>
<p>Note that the <a class="reference internal" href="velocity.html"><em>velocity</em></a> command can be used to create
velocities with zero aggregate linear and/or angular momentum.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">This fix performs its operations at the same point in
the timestep as other time integration fixes, such as <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, or <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>.
= middle of the box. The default is to use lattice units.
</P>
<P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
velocities with zero aggregate linear and/or angular momentum.
</P>
<P>IMPORTANT NOTE: This fix performs its operations at the same point in
the timestep as other time integration fixes, such as <A HREF = "fix_nve.html">fix
nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, or <A HREF = "fix_nh.html">fix npt</A>.
Thus fix recenter should normally be the last such fix specified in
the input script, since the adjustments it makes to atom coordinates
should come after the changes made by time integration. LAMMPS will
warn you if your fixes are not ordered this way.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you use this fix on a small group of atoms (e.g. a
molecule in solvent) without using the <em>shift</em> keyword to adjust the
warn you if your fixes are not ordered this way.
</P>
<P>IMPORTANT NOTE: If you use this fix on a small group of atoms (e.g. a
molecule in solvent) without using the <I>shift</I> keyword to adjust the
positions of all atoms in the system, then the results can be
unpredictable. For example, if the molecule is pushed in one
direction by the solvent, its velocity will increase. But its
coordinates will be recentered, meaning it is pushed back towards the
force. Thus over time, the velocity and temperature of the molecule
could become very large (though it won&#8217;t appear to be moving due to
could become very large (though it won't appear to be moving due to
the recentering). If you are thermostatting the entire system, then
the solvent would be cooled to compensate. A better solution for this
simulation scenario is to use the <a class="reference internal" href="fix_spring.html"><em>fix spring</em></a> command
to tether the molecule in place.</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<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline"></a></h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. 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 global scalar which can be accessed by various
<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar is the
distance the group is moved by fix recenter.</p>
<p>This fix also computes global 3-vector which can be accessed by
various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The 3
simulation scenario is to use the <A HREF = "fix_spring.html">fix spring</A> command
to tether the molecule in place.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
distance the group is moved by fix recenter.
</P>
<P>This fix also computes global 3-vector which can be accessed by
various <A HREF = "Section_howto.html#howto_15">output commands</A>. The 3
quantities in the vector are xyz components of displacement applied to
the group of atoms by the fix.</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"><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 should not be used with an x,y,z setting that causes a large
the group of atoms by the fix.
</P>
<P>The scalar and vector values calculated by this fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix should not be used with an x,y,z setting that causes a large
shift in the system on the 1st timestep, due to the requested COM
being very different from the initial COM. This could cause atoms to
be lost, especially in parallel. Instead, use the
<a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a> command, which can be used to
move atoms a large distance.</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_momentum.html"><em>fix momentum</em></a>, <a class="reference internal" href="velocity.html"><em>velocity</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are shift = fix group-ID, and units = lattice.</p>
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<A HREF = "displace_atoms.html">displace_atoms</A> command, which can be used to
move atoms a large distance.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_momentum.html">fix momentum</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are shift = fix group-ID, and units = lattice.
</P>
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