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General parameters and input/output files

Here, we document the syntax of the commands and parameters used to set up and use the collective variables module in NAMD. One of these parameters is the configuration file or the configuration text for the module itself, whose syntax is described in 10.1.2 and in the following sections.


Using the cv command

The colvars module is accessed in VMD through the command cv. The command must be used the first time as cv molid $ <$ molid$ >$ to set up the collective variables module for a given molecule. In all following uses, the cv command will continue operating on the same molecule, regardless of its ``top'' status. To use the cv command on a different molecule, use cv delete first and then cv molid $ <$ molid$ >$ . Invoking the cv command with no arguments prints a help screen.

Collective variables and biases can be added, queried and deleted through the scripting command cv, with the following syntax: cv $ <$ subcommand$ >$ [args...]. For example, to query the value of a collective variable named myVar, use the following syntax: set value [cv colvar myVar value]. All subcommands of cv are documented below.



Managing the colvars module

Input and output

Accessing collective variables

Accessing biases

NAMD parameters

To enable a collective variables-based calculation, two parameters must be added to the NAMD configuration file, colvars and colvarsConfig. An optional third parameter, colvarsInput, can be used to continue a previous simulation.

Configuration syntax for the collective variables module

All the parameters defining the colvars and their biasing or analysis algorithms are read from the file specified by colvarsConfig. Hence, none of the keywords described in this section and the following ones are available as keywords for the NAMD configuration file. The syntax of the colvars configuration is ``keyword value'', where the keyword and its value are separated by any white space. The following rules apply:

The following keywords are available in the global context of the colvars configuration, i.e. they are not nested inside other keywords:

The example below defines the same configuration shown in Fig. 6. The options within the colvar blocks are described in 10.2 and 10.4, the ones within the harmonic and histogram blocks in 10.5. Note: except colvar, none of the keywords shown is mandatory.

colvar {
  # difference of two distances
  name d
  width 0.2 # 0.2 Å of estimated fluctuation width
  distance {
    componentCoeff 1.0
    group1 { atomNumbers 1 2 }
    group2 { atomNumbers 3 4 5 }
  distance {
    componentCoeff -1.0
    group1 { atomNumbers 7 }
    group2 { atomNumbers 8 9 10 }

colvar {
  name c
  coordNum {
    cutoff 6.0
    group1 { atomNumbersRange 1-10 }
    group2 { atomNumbersRange 11-20 }

colvar {
  name alpha
  alpha {
    psfSegID PROT
    residueRange 1-10

harmonic {
  colvars d c
  centers 3.0 4.0
  forceConstant 5.0

histogram {
  colvars c alpha

Section 10.2 explains how to define a colvar and its behavior, regardless of its specific functional form. To define colvars that are appropriate to a specific physical system, Section 10.3 documents how to select atoms, and section 10.4 lists all of the available functional forms, which we call ``colvar components''. Finally, section 10.5 lists the available methods and algorithms to perform biased simulations and multidimensional analysis of colvars.

Input state file (optional)

Aside from the colvars configuration, an optional input state file may be provided to load the relevant data from a previous simulation. The name of this file is provided as a value to the keyword colvarsInput.

Output files

During a simulation with collective variables defined, the following three output files are written:

Other output files may be written by specific methods applied to the colvars (e.g. by the ABF method, see 10.5.1, or the metadynamics method, see 10.5.2). Like the colvar trajectory file, they are needed only for analyzing, not continuing a simulation. All such files' names also begin with the prefix outputName.

Finally, the total energy of all biases or restraints applied to the colvars appears under the NAMD standard output, under the MISC column.

next up previous contents index
Next: Defining collective variables and Up: Collective Variable-based Calculations1 Previous: Collective Variable-based Calculations1   Contents   Index