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@ -35,18 +35,21 @@ Examples
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Description
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"""""""""""
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This fix interfaces LAMMPS to the collective variables (Colvars) library,
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which allows to calculate potentials of mean force (PMFs) for any set of
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colvars, using sampling methods, including but not limited to Adaptive
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Biasing Force (ABF), metadynamics (MtD), Steered Molecular Dynamics (SMD)
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and Umbrella Sampling (US) via a flexible harmonic restraint bias.
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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 sampling methods, including but not limited to
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Adaptive Biasing Force (ABF), metadynamics (MtD), Steered Molecular
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Dynamics (SMD) and Umbrella Sampling (US) via a flexible harmonic
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restraint bias.
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This documentation describes only the ``fix colvars`` command itself in a
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LAMMPS script. The Colvars library is documented via the included
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`PDF manual <PDF/colvars-refman-lammps.pdf>`_ or at the webpage `https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html <https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html>`_.
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This documentation describes only the ``fix colvars`` command itself in
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a LAMMPS script. The Colvars library is documented via the included
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`PDF manual <PDF/colvars-refman-lammps.pdf>`_ or at the webpage
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`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html
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<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html>`_.
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The Colvars library is developed at `https://github.com/Colvars/colvars
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<https://github.com/Colvars/colvars>`_ A detailed discussion of its
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<https://github.com/Colvars/colvars>`_ A detailed discussion of its
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implementation is in :ref:`(Fiorin) <Fiorin>`; additional references are
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printed at runtime based on specific features being used.
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@ -55,79 +58,86 @@ There are some example scripts for using this package with LAMMPS in the
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----------
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The only required argument to ``fix colvars`` is the filename to the Colvars
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configuration file that contains the definition of the variables and any
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biasing methods applied to them.
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from the MD program in which the colvars library has been integrated.
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The only required argument to ``fix colvars`` is the filename to the
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Colvars configuration file that contains the definition of the variables
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and any biasing methods applied to them. from the MD program in which
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the colvars library has been integrated.
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The *group-ID* entry is ignored. ``fix colvars`` will always apply to the
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entire system, but specific atoms will be selected based on selection
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keywords in the Colvars configuration file or files. There is no need to
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define multiple ``fix colvars`` instances and it is not allowed.
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The *group-ID* entry is ignored. ``fix colvars`` will always apply to
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the entire system, but specific atoms will be selected based on
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selection keywords in the Colvars configuration file or files. There is
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no need to define multiple ``fix colvars`` instances and it is not
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allowed.
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The *output* keyword allows to specify the prefix of output files generated
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by Colvars, for example ``output.colvars.traj`` or ``output.pmf``.
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The *output* keyword allows to specify the prefix of output files
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generated by Colvars, for example ``output.colvars.traj`` or
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``output.pmf``.
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The *input* keyword allows to specify an optional state file that contains
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the restart information needed to continue a previous simulation state.
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Note, however, that ``fix colvars`` records its state in :doc:`binary restart
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<restart>` files, so when using the :doc:`read_restart <read_restart>`
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command, this is usually not needed.
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The *input* keyword allows to specify an optional state file that
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contains the restart information needed to continue a previous
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simulation state. Note, however, that ``fix colvars`` records its state
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in :doc:`binary restart <restart>` files, so when using the
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:doc:`read_restart <read_restart>` command, this is usually not needed.
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The *seed* keyword contains the seed for the random number generator used by
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Colvars.
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The *seed* keyword contains the seed for the random number generator
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used by Colvars.
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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. For information about when and how this affects results, please see `https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping <https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping>`_.
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the image flags to reconstruct the absolute atom positions. Setting
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this to *no* will use the current local coordinates that are wrapped
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back into the simulation cell at each re-neighboring instead. For
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information about when and how this affects results, please see
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`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping
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<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping>`_.
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The *tstat* keyword can be either NULL or the label of a thermostatting fix
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that thermostats all atoms in the fix colvars group. This will be used to
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let Colvars know what is the current thermostat target temperature.
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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 let Colvars know what is 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 :doc:`binary
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restart files <restart>`. This is in addition to the text mode
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``.colvars.state`` written by Colvars itself and the information in both
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files is identical.
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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 ``.colvars.state`` written by Colvars itself and the information in
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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 :doc:`fix_modify <fix_modify>` *energy* option is supported by this
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fix to add the energy change from the biasing force added by Colvars to
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the global potential energy of the system as part of :doc:`thermodynamic
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output <thermo_style>`. The default setting for this fix is
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:doc:`fix_modify energy no <fix_modify>`.
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The *fix_modify configfile <config file>* option loads Colvars configuration
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from an additional file. This option can only be used, after the system has
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been initialized with a :doc:`run <run>` command.
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The *fix_modify configfile <config file>* option loads Colvars
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configuration from an additional file. This option can only be used,
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after the system has been initialized with a :doc:`run <run>` 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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from inline strings. Those have to fit on a single line when enclosed in
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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
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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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:doc:`output commands <Howto_output>`. The scalar is the Colvars energy
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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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``fix colvars`` is provided by the COLVARS package and is only available if
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LAMMPS was built with that package. Some of the features also require code
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available from the LEPTON package. See the :doc:`Build package
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<Build_package>` page for more info.
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``fix colvars`` is provided by the COLVARS package and is only available
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if LAMMPS was built with that package. Some of the features also
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require code available from the LEPTON package. See the :doc:`Build
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package <Build_package>` page for more info.
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There can only be one Colvars instance defined at a time. Since the
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interface communicates only the minimum amount of information and the Colvars
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module itself can handle an arbitrary number of collective variables, this is
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not a limitation of functionality.
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interface communicates only the minimum amount of information and the
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Colvars module itself can handle an arbitrary number of collective
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variables, this is not a limitation of functionality.
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Related commands
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""""""""""""""""
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Axel Kohlmeyer