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 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 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.

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

The Colvars library is developed at https://github.com/colvars/colvars A detailed discussion of its implementation is in (Fiorin).

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 functionality 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 binary restart files, so when using the 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 thermostatting 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 binary restart files. 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 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 thermodynamic output.

The fix_modify configfile <config file> option allows to add settings from an additional config file to the colvars module. 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 cumulative 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 Build package doc page 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.

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