forked from lijiext/lammps
137 lines
5.3 KiB
Plaintext
137 lines
5.3 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: yes)
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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 mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
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fix abf all colvars colvars.inp tstat 1 :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. The colvars library is
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hosted at "http://colvars.github.io/"_http://colvars.github.io/
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This documentation describes only the fix colvars command itself and
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LAMMPS specific parts of the code. The full documentation of the
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colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf
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A detailed discussion of the implementation of the portable collective
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variable library is in "(Fiorin)"_#Fiorin. Additional information can
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be found in "(Henin)"_#Henin.
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There are some example scripts for using this package with LAMMPS in the
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examples/USER/colvars directory.
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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 the 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 and there can only be one instance
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of the colvars fix at a time. The colvars fix will only communicate
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the minimum information necessary and the colvars library supports
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multiple, completely independent collective variables, so there is
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no restriction to functionaliry by limiting the number of colvars fixes.
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The {input} keyword allows to specify a state file that would contain
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the restart information required in order to continue a calculation from
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a prerecorded state. Fix colvars records it state in "binary restart"_restart.html
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files, so when using the "read_restart"_read_restart.html command,
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this is usually not needed.
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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 {yes}, i.e. to use
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the image flags to reconstruct the absolute atom positions.
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Setting this to {no} will use the current local coordinates that are
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wrapped back into the simulation cell at each re-neighboring instead.
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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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This fix writes the current status of the colvars module into
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"binary restart files"_restart.html. This is in addition to the text
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mode status file that is written by the colvars module itself and the
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kind of information in both files is identical.
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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 interface
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communicates only the minimum amount of information and colvars module
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itself can handle an arbitrary number of collective variables, this is
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not a limitation of functionality.
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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, unwrap yes,
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and tstat = NULL.
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:line
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:link(Fiorin)
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[(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
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:link(Henin)
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[(Henin)] Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
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35-47 (2010)
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