forked from lijiext/lammps
124 lines
4.5 KiB
Plaintext
124 lines
4.5 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix colvars command :h3
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[Syntax:]
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fix ID group-ID colvars configfile keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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colvars = style name of this fix command :l
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configfile = the configuration file for the colvars module :l
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keyword = {input} or {output} or {seed} or {tstat} :l
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{input} arg = colvars.state file name or prefix or NULL (default: NULL)
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{output} arg = output filename prefix (default: out)
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{seed} arg = seed for random number generator (default: 1966)
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{unwrap} arg = {yes} or {no}
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use unwrapped coordinates in collective variables (default: no)
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{tstat} arg = fix id of a thermostat or NULL (default: NULL) :pre
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:ule
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[Examples:]
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fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide unwrap yes
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fix colvars all colvars.inp :pre
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[Description:]
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This fix interfaces LAMMPS to a "collective variables" or "colvars"
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module library which allows to calculate potentials of mean force
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(PMFs) for any set of colvars, using different sampling methods:
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currently implemented are the Adaptive Biasing Force (ABF) method,
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metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
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(US) via a flexible harmonic restraint bias. This documentation
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describes only the colvars fix itself and LAMMPS specific parts of the
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code. The documentation of the colvars implementation itself is
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available as part of the "NAMD online
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documentation"_http://www.ks.uiuc.edu/Research/namd/2.8/ug/node53.html
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There are example scripts for using this package with LAMMPS in
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examples/USER/colvars.
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The implementation of the portable collective variable library is also
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documented in "(Henin)"_#Henin
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:line
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The only mandatory argument to the fix is the filename to the colvars
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input file that contains all input that is independent from the MD
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program in which the colvars library has been integrated.
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The {group-ID} entry is ignored. The collective variable module will
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always apply to the entire system, i.e. use the group {all}.
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The {input} keyword allows to specify a state file that would contain
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the information required in order to continue a calculation, e.g.
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from a restart. Setting it to NULL will start a new colvars run.
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The {output} keyword allows to specify the output prefix. All output
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files generated will use this prefix followed by the ".colvars." and
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a word like "state" or "traj".
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The {seed} keyword contains the seed for the random number generator
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that will be used in the colvars module.
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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 {no}, i.e. to use the
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current local coordinates that are wrapped back into the simulation cell
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at each re-neighboring. Setting this to {yes} will use the image flags
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to reconstruct the absolute atom positions.
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The {tstat} keyword can be either NULL or the label of a thermostating
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fix that thermostats all atoms in the fix colvars group. This will be
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used to provide the colvars module with 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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No information about this fix is written to "binary restart
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files"_restart.html.
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The "fix_modify"_fix_modify.html {energy} option is supported by this
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fix to add the energy change from the biasing force added by the fix
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to the system's potential energy as part of "thermodynamic
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output"_thermo_style.html.
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This fix computes a global scalar which can be accessed by various
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"output commands"_Section_howto.html#howto_15. The scalar is the
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cummulative energy change due to this fix. The scalar value
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calculated by this fix is "extensive".
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[Restrictions:]
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This fix is part of the USER-COLVARS package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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There can only be one colvars fix active at a time. Since the
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colvars module itself can handle an arbitrary number of collective
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variables and always applies to the entire system, this is not
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really a deficit in practice.
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[Related commands:]
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"fix smd"_fix_smd.html
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[Default:]
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The default options are input = NULL, output = out, seed = 1966, and
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tstat = NULL.
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:line
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:link(Henin)
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[(Henin)] Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
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35-47 (2010)
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