forked from lijiext/lammps
159 lines
5.5 KiB
Plaintext
159 lines
5.5 KiB
Plaintext
.. index:: fix colvars
|
|
|
|
fix colvars command
|
|
===================
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix ID group-ID colvars configfile keyword values ...
|
|
|
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
|
* colvars = style name of this fix command
|
|
* configfile = the configuration file for the colvars module
|
|
* keyword = *input* or *output* or *seed* or *tstat*
|
|
.. parsed-literal::
|
|
|
|
*input* arg = colvars.state file name or prefix or NULL (default: NULL)
|
|
*output* arg = output filename prefix (default: out)
|
|
*seed* arg = seed for random number generator (default: 1966)
|
|
*unwrap* arg = *yes* or *no*
|
|
use unwrapped coordinates in collective variables (default: yes)
|
|
*tstat* arg = fix id of a thermostat or NULL (default: NULL)
|
|
|
|
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
|
|
fix abf all colvars colvars.inp tstat 1
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
This fix interfaces LAMMPS to a "collective variables" or "colvars"
|
|
module library which allows to calculate potentials of mean force
|
|
(PMFs) for any set of colvars, using different sampling methods:
|
|
currently implemented are the Adaptive Biasing Force (ABF) method,
|
|
metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
|
|
(US) via a flexible harmonic restraint bias. The colvars library is
|
|
hosted at `http://colvars.github.io/ <http://colvars.github.io/>`_
|
|
|
|
This documentation describes only the fix colvars command itself and
|
|
LAMMPS specific parts of the code. The full documentation of the
|
|
colvars library is available as `this supplementary PDF document <PDF/colvars-refman-lammps.pdf>`_
|
|
|
|
A detailed discussion of the implementation of the portable collective
|
|
variable library is in :ref:`(Fiorin) <Fiorin>`. Additional information can
|
|
be found in :ref:`(Henin) <Henin>`.
|
|
|
|
There are some example scripts for using this package with LAMMPS in the
|
|
examples/USER/colvars directory.
|
|
|
|
|
|
----------
|
|
|
|
|
|
The only mandatory argument to the fix is the filename to the colvars
|
|
input file that contains the input that is independent from the MD
|
|
program in which the colvars library has been integrated.
|
|
|
|
The *group-ID* entry is ignored. The collective variable module will
|
|
always apply to the entire system and there can only be one instance
|
|
of the colvars fix at a time. The colvars fix will only communicate
|
|
the minimum information necessary and the colvars library supports
|
|
multiple, completely independent collective variables, so there is
|
|
no restriction to functionaliry by limiting the number of colvars fixes.
|
|
|
|
The *input* keyword allows to specify a state file that would contain
|
|
the restart information required in order to continue a calculation from
|
|
a prerecorded state. Fix colvars records it state in :doc:`binary restart <restart>`
|
|
files, so when using the :doc:`read_restart <read_restart>` command,
|
|
this is usually not needed.
|
|
|
|
The *output* keyword allows to specify the output prefix. All output
|
|
files generated will use this prefix followed by the ".colvars." and
|
|
a word like "state" or "traj".
|
|
|
|
The *seed* keyword contains the seed for the random number generator
|
|
that will be used in the colvars module.
|
|
|
|
The *unwrap* keyword controls whether wrapped or unwrapped coordinates
|
|
are passed to the colvars library for calculation of the collective
|
|
variables and the resulting forces. The default is *yes*, i.e. to use
|
|
the image flags to reconstruct the absolute atom positions.
|
|
Setting this to *no* will use the current local coordinates that are
|
|
wrapped back into the simulation cell at each re-neighboring instead.
|
|
|
|
The *tstat* keyword can be either NULL or the label of a thermostating
|
|
fix that thermostats all atoms in the fix colvars group. This will be
|
|
used to provide the colvars module with the current thermostat target
|
|
temperature.
|
|
|
|
Restart, fix_modify, output, run start/stop, minimize info
|
|
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
|
|
|
This fix writes the current status of the colvars module into
|
|
:doc:`binary restart files <restart>`. This is in addition to the text
|
|
mode status file that is written by the colvars module itself and the
|
|
kind of information in both files is identical.
|
|
|
|
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
|
|
fix to add the energy change from the biasing force added by the fix
|
|
to the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
|
|
|
|
This fix computes a global scalar which can be accessed by various
|
|
:ref:`output commands <howto_15>`. The scalar is the
|
|
cummulative energy change due to this fix. The scalar value
|
|
calculated by this fix is "extensive".
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
|
|
|
|
This fix is part of the USER-COLVARS package. It is only enabled if
|
|
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
|
|
|
|
There can only be one colvars fix active at a time. Since the interface
|
|
communicates only the minimum amount of information and colvars module
|
|
itself can handle an arbitrary number of collective variables, this is
|
|
not a limitation of functionality.
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`fix smd <fix_smd>`
|
|
|
|
Default
|
|
"""""""
|
|
|
|
The default options are input = NULL, output = out, seed = 1966, unwrap yes,
|
|
and tstat = NULL.
|
|
|
|
|
|
----------
|
|
|
|
|
|
.. _Fiorin:
|
|
|
|
|
|
|
|
**(Fiorin)** Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
|
|
|
|
.. _Henin:
|
|
|
|
|
|
|
|
**(Henin)** Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
|
|
35-47 (2010)
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|