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<div class="section" id="fix-colvars-command">
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<span id="index-0"></span><h1>fix colvars command<a class="headerlink" href="#fix-colvars-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 colvars configfile 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>colvars = style name of this fix command</li>
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<li>configfile = the configuration file for the colvars module</li>
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<li>keyword = <em>input</em> or <em>output</em> or <em>seed</em> or <em>tstat</em></li>
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</ul>
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<pre class="literal-block">
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<em>input</em> arg = colvars.state file name or prefix or NULL (default: NULL)
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<em>output</em> arg = output filename prefix (default: out)
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<em>seed</em> arg = seed for random number generator (default: 1966)
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<em>unwrap</em> arg = <em>yes</em> or <em>no</em>
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use unwrapped coordinates in collective variables (default: yes)
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<em>tstat</em> arg = fix id of a thermostat or NULL (default: NULL)
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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 mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
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fix abf all colvars colvars.inp tstat 1
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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>This fix interfaces LAMMPS to a “collective variables” or “colvars”
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module library which allows to calculate potentials of mean force
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(PMFs) for any set of colvars, using different sampling methods:
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currently implemented are the Adaptive Biasing Force (ABF) method,
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metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
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(US) via a flexible harmonic restraint bias. The colvars library is
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hosted at <a class="reference external" href="http://colvars.github.io/">http://colvars.github.io/</a></p>
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<p>This documentation describes only the fix colvars command itself and
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LAMMPS specific parts of the code. The full documentation of the
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colvars library is available as <a class="reference external" href="PDF/colvars-refman-lammps.pdf">this supplementary PDF document</a></p>
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<p>A detailed discussion of the implementation of the portable collective
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variable library is in <a class="reference internal" href="#fiorin"><span>(Fiorin)</span></a>. Additional information can
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be found in <a class="reference internal" href="#henin"><span>(Henin)</span></a>.</p>
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<p>There are some example scripts for using this package with LAMMPS in the
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examples/USER/colvars directory.</p>
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<hr class="docutils" />
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<p>The only mandatory argument to the fix is the filename to the colvars
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input file that contains the input that is independent from the MD
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program in which the colvars library has been integrated.</p>
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<p>The <em>group-ID</em> entry is ignored. The collective variable module will
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always apply to the entire system and there can only be one instance
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of the colvars fix at a time. The colvars fix will only communicate
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the minimum information necessary and the colvars library supports
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multiple, completely independent collective variables, so there is
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no restriction to functionaliry by limiting the number of colvars fixes.</p>
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<p>The <em>input</em> keyword allows to specify a state file that would contain
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the restart information required in order to continue a calculation from
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a prerecorded state. Fix colvars records it state in <a class="reference internal" href="restart.html"><em>binary restart</em></a>
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files, so when using the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command,
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this is usually not needed.</p>
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<p>The <em>output</em> keyword allows to specify the output prefix. All output
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files generated will use this prefix followed by the ”.colvars.” and
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a word like “state” or “traj”.</p>
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<p>The <em>seed</em> keyword contains the seed for the random number generator
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that will be used in the colvars module.</p>
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<p>The <em>unwrap</em> keyword controls whether wrapped or unwrapped coordinates
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are passed to the colvars library for calculation of the collective
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variables and the resulting forces. The default is <em>yes</em>, i.e. to use
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the image flags to reconstruct the absolute atom positions.
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Setting this to <em>no</em> will use the current local coordinates that are
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wrapped back into the simulation cell at each re-neighboring instead.</p>
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<p>The <em>tstat</em> keyword can be either NULL or the label of a thermostating
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fix that thermostats all atoms in the fix colvars group. This will be
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used to provide the colvars module with the current thermostat target
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temperature.</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>This fix writes the current status of the colvars module into
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<a class="reference internal" href="restart.html"><em>binary restart files</em></a>. This is in addition to the text
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mode status file that is written by the colvars module itself and the
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kind of information in both files is identical.</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 change from the biasing force added by the fix
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to the system’s potential 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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cummulative energy change due to this fix. The scalar value
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calculated by this fix is “extensive”.</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 fix is part of the USER-COLVARS package. It is only enabled if
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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>
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<p>There can only be one colvars fix active at a time. Since the interface
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communicates only the minimum amount of information and colvars module
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itself can handle an arbitrary number of collective variables, this is
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not a limitation of functionality.</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="fix_smd.html"><em>fix smd</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The default options are input = NULL, output = out, seed = 1966, unwrap yes,
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and tstat = NULL.</p>
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<hr class="docutils" />
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<p id="fiorin"><strong>(Fiorin)</strong> Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594</p>
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<p id="henin"><strong>(Henin)</strong> Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
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35-47 (2010)</p>
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