fix ID group-ID colvars configfile keyword values ...
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)
fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide fix abf all colvars colvars.inp tstat 1
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. This documentation describes only the colvars fix itself and LAMMPS specific parts of the code. The documentation of the colvars implementation itself is available as part of the NAMD online documentation
There are example scripts for using this package with LAMMPS in examples/USER/colvars.
The implementation of the portable collective variable library is also documented in (Henin)
The only mandatory argument to the fix is the filename to the colvars input file that contains all 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, i.e. use the group all.
The input keyword allows to specify a state file that would contain the information required in order to continue a calculation, e.g. from a restart. Setting it to NULL will start a new colvars run.
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:
No information about this fix is written to binary restart files.
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.
This fix computes a global scalar which can be accessed by various output commands. The scalar is the cummulative energy change due to this fix. The scalar value calculated by this fix is "extensive".
This fix is part of the USER-COLVARS package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
There can only be one colvars fix active at a time. Since the colvars module itself can handle an arbitrary number of collective variables and always applies to the entire system, this is not really a deficit in practice.
The default options are input = NULL, output = out, seed = 1966, unwrap yes, and tstat = NULL.
(Henin) Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, 35-47 (2010)