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<div class="section" id="fix-neb-command">
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<span id="index-0"></span><h1>fix neb command<a class="headerlink" href="#fix-neb-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 neb Kspring
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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>neb = style name of this fix command</li>
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<li>Kspring = inter-replica spring constant (force/distance units)</li>
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</ul>
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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 1 active neb 10.0
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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>Add inter-replica forces to atoms in the group for a multi-replica
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simulation run via the <a class="reference internal" href="neb.html"><em>neb</em></a> command to perform a nudged
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elastic band (NEB) calculation for transition state finding. Hi-level
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explanations of NEB are given with the <a class="reference internal" href="neb.html"><em>neb</em></a> command and in
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<a class="reference internal" href="Section_howto.html#howto-5"><span>Section_howto 5</span></a> of the manual. The fix
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neb command must be used with the “neb” command to define how
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inter-replica forces are computed.</p>
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<p>Only the N atoms in the fix group experience inter-replica forces.
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Atoms in the two end-point replicas do not experience these forces,
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but those in intermediate replicas do. During the initial stage of
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NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
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on the atoms of each intermediate replica I is altered, as described
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in the <a class="reference internal" href="neb.html#henkelman1"><span>(Henkelman1)</span></a> paper, to become:</p>
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<div class="highlight-python"><div class="highlight"><pre>Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That
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</pre></div>
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</div>
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<p>Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
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coordinates of its neighbor replicas. That (t with a hat over it) is
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the unit “tangent” vector for replica I which is a function of Ri,
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Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
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roughly in the direction of (Ri+i - Ri-1); see the
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<a class="reference internal" href="neb.html#henkelman1"><span>(Henkelman1)</span></a> paper for details.</p>
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<p>The first two terms in the above equation are the component of the
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interatomic forces perpendicular to the tangent vector. The last term
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is a spring force between replica I and its neighbors, parallel to the
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tangent vector direction with the specified spring constant <em>Kspring</em>.</p>
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<p>The effect of the first two terms is to push the atoms of each replica
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toward the minimum energy path (MEP) of conformational states that
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transition over the energy barrier. The MEP for an energy barrier is
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defined as a sequence of 3N-dimensional states which cross the barrier
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at its saddle point, each of which has a potential energy gradient
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parallel to the MEP itself.</p>
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<p>The effect of the last term is to push each replica away from its two
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neighbors in a direction along the MEP, so that the final set of
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states are equidistant from each other.</p>
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<p>During the second stage of NEB, the forces on the N atoms in the
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replica nearest the top of the energy barrier are altered so that it
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climbs to the top of the barrier and finds the saddle point. The
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forces on atoms in this replica are described in the
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<a class="reference internal" href="neb.html#henkelman2"><span>(Henkelman2)</span></a> paper, and become:</p>
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<div class="highlight-python"><div class="highlight"><pre>Fi = -Grad(V) + 2 (Grad(V) dot That) That
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</pre></div>
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</div>
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<p>The inter-replica forces for the other replicas are unchanged from the
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first equation.</p>
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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>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. No parameter of this fix can
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be used with the <em>start/stop</em> keywords of 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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as invoked by the <a class="reference internal" href="minimize.html"><em>minimize</em></a> command via the
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<a class="reference internal" href="neb.html"><em>neb</em></a> command.</p>
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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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<p>This command can only be used if LAMMPS was built with the REPLICA
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package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
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for more info on packages.</p>
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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="neb.html"><em>neb</em></a></p>
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<p><strong>Default:</strong> none</p>
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<p id="henkelman"><strong>(Henkelman1)</strong> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).</p>
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<p id="id1"><strong>(Henkelman2)</strong> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
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9901-9904 (2000).</p>
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