Subsections

• Commands to manage the Colvars module
• Commands to manage individual collective variables
• Commands to manage individual biases

Scripting interface (Tcl): list of commands

This section lists all the commands used in NAMD to control the behavior of the Colvars module from within a run script.

Commands to manage the Colvars module

• cv addenergy <E>
  Add an energy to the MD engine (no effect in VMD)
  Parameters
  E : float - Amount of energy to add
• cv config <conf>
  Read configuration from the given string
  Parameters
  conf : string - Configuration string
• cv configfile <conf_file>
  Read configuration from a file
  Parameters
  conf_file : string - Path to configuration file
• cv delete
  Delete this Colvars module instance (VMD only)
• cv frame [frame]
  Get or set current frame number (VMD only)
  Parameters
  frame : integer - Frame number (optional)
• cv getconfig
  Get the module's configuration string read so far
• cv getenergy
  Get the current Colvars energy
• cv help [command]
  Get the help string of the Colvars scripting interface
  Parameters
  command : string - Get the help string of this specific command (optional)
• cv list [param]
  Return a list of all variables or biases
  Parameters
  param : string - "colvars" or "biases"; default is "colvars" (optional)
• cv listcommands
  Get the list of script functions, prefixed with "cv_", "colvar_" or "bias_"
• cv load <prefix>
  Load data from a state file into all matching colvars and biases
  Parameters
  prefix : string - Path to existing state file or input prefix
• cv loadfromstring <buffer>
  Load state data from a string into all matching colvars and biases
  Parameters
  buffer : string - String buffer containing the state information
• cv molid [molid]
  Get or set the molecule ID on which Colvars is defined (VMD only)
  Parameters
  molid : integer - Molecule ID; -1 means undefined (optional)
• cv printframe
  Return the values that would be written to colvars.traj
• cv printframelabels
  Return the labels that would be written to colvars.traj
• cv reset
  Delete all internal configuration
• cv resetindexgroups
  Clear the index groups loaded so far, allowing to replace them
• cv save <prefix>
  Change the prefix of all output files and save them
  Parameters
  prefix : string - Output prefix with trailing ".colvars.state" gets removed)
• cv savetostring
  Write the Colvars state to a string and return it
• cv units [units]
  Get or set the current Colvars unit system
  Parameters
  units : string - The new unit system (optional)
• cv update
  Recalculate colvars and biases
• cv version
  Get the Colvars Module version number

Commands to manage individual collective variables

• cv colvar name addforce <force>
  Apply the given force onto this colvar and return the same
  Parameters
  force : float or array - Applied force; must match colvar dimensionality
• cv colvar name cvcflags <flags>
  Enable or disable individual components by setting their active flags
  Parameters
  flags : integer array - Zero/nonzero value disables/enables the CVC
• cv colvar name delete
  Delete this colvar, along with all biases that depend on it
• cv colvar name get <feature>
  Get the value of the given feature for this colvar
  Parameters
  feature : string - Name of the feature
• cv colvar name getappliedforce
  Return the total of the forces applied to this colvar
• cv colvar name getatomgroups
  Return the atom indices used by this colvar as a list of lists
• cv colvar name getatomids
  Return the list of atom indices used by this colvar
• cv colvar name getconfig
  Return the configuration string of this colvar
• cv colvar name getgradients
  Return the atomic gradients of this colvar
• cv colvar name gettotalforce
  Return the sum of internal and external forces to this colvar
• cv colvar name help [command]
  Get a help summary or the help string of one colvar subcommand
  Parameters
  command : string - Get the help string of this specific command (optional)
• cv colvar name modifycvcs <confs>
  Modify configuration of individual components by passing string arguments
  Parameters
  confs : sequence of strings - New configurations; empty strings are skipped
• cv colvar name run_ave
  Get the current running average of the value of this colvar
• cv colvar name set <feature> <value>
  Set the given feature of this colvar to a new value
  Parameters
  feature : string - Name of the feature
  value : string - String representation of the new feature value
• cv colvar name state
  Print a string representation of the feature state of this colvar
• cv colvar name type
  Get the type description of this colvar
• cv colvar name update
  Recompute this colvar and return its up-to-date value
• cv colvar name value
  Get the current value of this colvar
• cv colvar name width
  Get the width of this colvar

Commands to manage individual biases

• cv bias name bin
  Get the current grid bin index (1D ABF only for now)
• cv bias name bincount [index]
  Get the number of samples at the given grid bin (1D ABF only for now)
  Parameters
  index : integer - Grid index; defaults to current bin (optional)
• cv bias name binnum
  Get the total number of grid points of this bias (1D ABF only for now)
• cv bias name delete
  Delete this bias
• cv bias name energy
  Get the current energy of this bias
• cv bias name get <feature>
  Get the value of the given feature for this bias
  Parameters
  feature : string - Name of the feature
• cv bias name getconfig
  Return the configuration string of this bias
• cv bias name help [command]
  Get a help summary or the help string of one bias subcommand
  Parameters
  command : string - Get the help string of this specific command (optional)
• cv bias name load <prefix>
  Load data into this bias
  Parameters
  prefix : string - Read from a file with this name or prefix
• cv bias name loadfromstring <buffer>
  Load state data into this bias from a string
  Parameters
  buffer : string - String buffer containing the state information
• cv bias name save <prefix>
  Save data from this bias into a file with the given prefix
  Parameters
  prefix : string - Prefix for the state file of this bias
• cv bias name savetostring
  Save data from this bias into a string and return it
• cv bias name set <feature> <value>
  Set the given feature of this bias to a new value
  Parameters
  feature : string - Name of the feature
  value : string - String representation of the new feature value
• cv bias name share
  Share bias information with other replicas (multiple-walker scheme)
• cv bias name state
  Print a string representation of the feature state of this bias
• cv bias name update
  Recompute this bias and return its up-to-date energy