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fix colvars command

Syntax

fix ID group-ID colvars configfile keyword values ...

  • ID, group-ID are documented in fix command

  • colvars = style name of this fix command

  • configfile = the configuration file for the colvars module

  • keyword = input or output or seed or unwrap or tstat

    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

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 the collective variables (Colvars) library, which allows to calculate potentials of mean force (PMFs) for any set of colvars, using sampling methods, including but not limited to Adaptive Biasing Force (ABF), metadynamics (MtD), Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) via a flexible harmonic restraint bias.

This documentation describes only the fix colvars command itself in a LAMMPS script. The Colvars library is documented via the included PDF manual or at the webpage https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html.

The Colvars library is developed at https://github.com/Colvars/colvars A detailed discussion of its implementation is in (Fiorin); additional references are printed at runtime based on specific features being used.

There are some example scripts for using this package with LAMMPS in the examples/PACKAGES/colvars directory.

The only required argument to fix colvars is the filename to the Colvars configuration file that contains the definition of the variables and any biasing methods applied to them. from the MD program in which the colvars library has been integrated.

The group-ID entry is ignored. fix colvars will always apply to the entire system, but specific atoms will be selected based on selection keywords in the Colvars configuration file or files. There is no need to define multiple fix colvars instances and it is not allowed.

The output keyword allows to specify the prefix of output files generated by Colvars, for example output.colvars.traj or output.pmf.

The input keyword allows to specify an optional state file that contains the restart information needed to continue a previous simulation state. Note, however, that fix colvars records its state in binary restart files, so when using the read_restart command, this is usually not needed.

The seed keyword contains the seed for the random number generator used by Colvars.

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. 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.

The tstat keyword can be either NULL or the label of a thermostatting fix that thermostats all atoms in the fix colvars group. This will be used to let Colvars know what is 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 binary restart files. This is in addition to the text mode .colvars.state written by Colvars itself and the information in both files is identical.

The fix_modify energy option is supported by this fix to add the energy change from the biasing force added by Colvars to the global potential energy of the system as part of thermodynamic output. The default setting for this fix is fix_modify energy no.

The fix_modify configfile <config file> option loads Colvars configuration from an additional file. This option can only be used, after the system has been initialized with a run command.

The fix_modify config <quoted string> option allows to add settings from inline strings. Those have to fit on a single line when enclosed in a pair of double quotes (“), or can span multiple lines when bracketed by a pair of triple double quotes (“””, like Python embedded documentation).

This fix computes a global scalar which can be accessed by various output commands. The scalar is the Colvars energy mentioned above. The scalar value calculated by this fix is “extensive”.

Restrictions

fix colvars is provided by the COLVARS package and is only available if LAMMPS was built with that package. Some of the features also require code available from the LEPTON package. See the Build package page for more info.

There can only be one Colvars instance defined at a time. Since the interface communicates only the minimum amount of information and the Colvars module itself can handle an arbitrary number of collective variables, this is not a limitation of functionality.

Default

The default options are input = NULL, output = out, seed = 1966, unwrap yes, and tstat = NULL.

(Fiorin) Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594