forked from lijiext/lammps
125 lines
4.5 KiB
HTML
125 lines
4.5 KiB
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>fix colvars command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID colvars configfile keyword values ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>colvars = style name of this fix command
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<LI>configfile = the configuration file for the colvars module
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<LI>keyword = <I>input</I> or <I>output</I> or <I>seed</I> or <I>tstat</I>
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<PRE> <I>input</I> arg = colvars.state file name or prefix or NULL (default: NULL)
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<I>output</I> arg = output filename prefix (default: out)
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<I>seed</I> arg = seed for random number generator (default: 1966)
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<I>tstat</I> arg = fix id of a thermostat or NULL (default: NULL)
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
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fix colvars all colvars.inp
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</PRE>
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<P><B>Description:</B>
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</P>
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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. This documentation
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describes only the colvars fix itself and LAMMPS specific parts of the
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code. The documentation of the colvars implementation itself is
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available as part of the <A HREF = "http://www.ks.uiuc.edu/Research/namd/2.8/ug/node53.html">NAMD online
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documentation</A>
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</P>
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<P>There are example scripts for using this package with LAMMPS in
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examples/USER/colvars.
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</P>
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<P>The implementation of the portable collective variable library is also
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documented in <A HREF = "#Henin">(Henin)</A>
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</P>
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<HR>
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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 all input that is independent from the MD
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program in which the colvars library has been integrated.
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</P>
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<P>The <I>group-ID</I> entry is ignored. The collective variable module will
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always apply to the entire system, i.e. use the group <I>all</I>.
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</P>
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<P>The <I>input</I> keyword allows to specify a state file that would contain
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the information required in order to continue a calculation, e.g.
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from a restart. Setting it to NULL will start a new colvars run.
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</P>
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<P>The <I>output</I> 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".
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</P>
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<P>The <I>seed</I> keyword contains the seed for the random number generator
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that will be used in the colvars module.
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</P>
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<P>The <I>tstat</I> 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.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> 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 HREF = "thermo_style.html">thermodynamic
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output</A>.
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</P>
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<P>This fix computes a global scalar which can be accessed by various
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<A HREF = "Section_howto.html#howto_15">output commands</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".
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</P>
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<P><B>Restrictions:</B>
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</P>
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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 HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P>There can only be one colvars fix active at a time. Since the
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colvars module itself can handle an arbitrary number of collective
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variables and always applies to the entire system, this is not
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really a deficit in practice.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_smd.html">fix smd</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The default options are input = NULL, output = out, seed = 1966, and
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tstat = NULL.
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</P>
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<HR>
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<A NAME = "Henin"></A>
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<P><B>(Henin)</B> Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
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35-47 (2010)
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</P>
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</HTML>
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