forked from lijiext/lammps
148 lines
5.9 KiB
HTML
148 lines
5.9 KiB
HTML
<HTML>
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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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<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>unwrap</I> arg = <I>yes</I> or <I>no</I>
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use unwrapped coordinates in collective variables (default: yes)
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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 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>
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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. The colvars library is
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hosted at <A HREF = "http://colvars.github.io/">http://colvars.github.io/</A>
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</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 HREF = "PDF/colvars-refman-lammps.pdf">this supplementary PDF document</A>
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</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 HREF = "#Fiorin">(Fiorin)</A>. Additional information can
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be found in <A HREF = "#Henin">(Henin)</A>.
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</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.
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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 the 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 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.
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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 restart information required in order to continue a calculation from
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a prerecorded state. Fix colvars records it state in <A HREF = "restart.html">binary restart</A>
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files, so when using the <A HREF = "read_restart.html">read_restart</A> command,
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this is usually not needed.
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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>unwrap</I> 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 <I>yes</I>, i.e. to use
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the image flags to reconstruct the absolute atom positions.
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Setting this to <I>no</I> will use the current local coordinates that are
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wrapped back into the simulation cell at each re-neighboring instead.
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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>This fix writes the current status of the colvars module into
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<A HREF = "restart.html">binary restart files</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.
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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 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.
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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, unwrap yes,
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and tstat = NULL.
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</P>
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<HR>
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<A NAME = "Fiorin"></A>
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<P><B>(Fiorin)</B> Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
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</P>
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<A NAME = "Henin"></A>
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<P><B>(Henin)</B> Henin, 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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