151 lines
5.8 KiB
ReStructuredText
151 lines
5.8 KiB
ReStructuredText
.. index:: fix colvars
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fix colvars command
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===================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID colvars configfile keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* colvars = style name of this fix command
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* configfile = the configuration file for the colvars module
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* keyword = *input* or *output* or *seed* or *tstat*
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.. parsed-literal::
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*input* arg = colvars.state file name or prefix or NULL (default: NULL)
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*output* arg = output filename prefix (default: out)
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*seed* arg = seed for random number generator (default: 1966)
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*unwrap* arg = *yes* or *no*
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use unwrapped coordinates in collective variables (default: yes)
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*tstat* arg = fix id of a thermostat or NULL (default: NULL)
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Examples
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""""""""
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.. code-block:: LAMMPS
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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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Description
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"""""""""""
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This fix interfaces LAMMPS to the collective variables (Colvars)
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library, which allows to calculate potentials of mean force (PMFs) for
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any set of colvars, using different sampling methods: currently
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implemented are the Adaptive Biasing Force (ABF) method, metadynamics,
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Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) via a
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flexible harmonic restraint bias.
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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 `this supplementary PDF document <PDF/colvars-refman-lammps.pdf>`_
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The Colvars library is developed at `https://github.com/colvars/colvars <https://github.com/colvars/colvars>`_
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A detailed discussion of its implementation is in :ref:`(Fiorin) <Fiorin>`.
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There are some example scripts for using this package with LAMMPS in the
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examples/PACKAGES/colvars directory.
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----------
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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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The *group-ID* 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 functionality by limiting the number of colvars fixes.
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The *input* 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 :doc:`binary restart <restart>`
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files, so when using the :doc:`read_restart <read_restart>` command,
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this is usually not needed.
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The *output* 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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The *seed* 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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The *unwrap* 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 *yes*, i.e. to use
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the image flags to reconstruct the absolute atom positions.
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Setting this to *no* 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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The *tstat* keyword can be either NULL or the label of a thermostatting
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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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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix writes the current status of the colvars module into
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:doc:`binary restart files <restart>`. 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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The :doc:`fix_modify <fix_modify>` *energy* option is supported by
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this fix to add the energy change from the biasing force added by
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Colvars to the global potential energy of the system as part of
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:doc:`thermodynamic output <thermo_style>`. The default setting for
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this fix is :doc:`fix_modify energy no <fix_modify>`.
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The *fix_modify configfile <config file>* option allows to add settings
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from an additional config file to the colvars module. This option can
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only be used, after the system has been initialized with a :doc:`run <run>`
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command.
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The *fix_modify config <quoted string>* option allows to add settings
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from inline strings. Those have to fit on a single line when enclosed
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in a pair of double quotes ("), or can span multiple lines when bracketed
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by a pair of triple double quotes (""", like python embedded documentation).
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This fix computes a global scalar which can be accessed by various
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:doc:`output commands <Howto_output>`. The scalar is the Colvars
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energy mentioned above. The scalar value calculated by this fix is
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"extensive".
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Restrictions
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""""""""""""
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This fix is part of the COLVARS package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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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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Related commands
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""""""""""""""""
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:doc:`fix smd <fix_smd>`, :doc:`fix spring <fix_spring>`,
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:doc:`fix plumed <fix_plumed>`
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Default
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"""""""
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The default options are input = NULL, output = out, seed = 1966, unwrap yes,
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and tstat = NULL.
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----------
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.. _Fiorin:
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**(Fiorin)** Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
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