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


General parameters and input/output files

The structure of a typical colvars configuration is represented in Figure 6. Each colvar is a combination of one or more components (see 10.2), which are functions of several atomic coordinates. Many different biasing or analysis methods can be applied to the same colvars. But care should be taken that certain methods (such as free energy reconstruction) do not produce correct results when other biases are adding forces to their colvars.

Figure 6: Example of a collective variables (colvar) configuration. The colvar ``$ d$'' is defined as the difference between two distances, each calculated between the centers of mass of two atom groups. The second colvar ``$ c$'' holds the coordination number (i.e. the number of contacts) within a radius of 6 Å between two groups. The third colvar ``alpha'' measures the degree of $ \alpha $-helicity of the protein segment between residues 1 and 10. A moving harmonic restraint is applied to the colvars ``$ d$'' and ``$ c$'', each rescaled by means of width parameters $ w_{d}$ and $ w_{c}$; the centers of the restraint, $ d_0$ and $ c_0$, evolve with the simulation time $ t$. The joint histogram of ``alpha'' and ``$ c$'' is also recorded on-the-fly.

NAMD parameters

To enable a colvar calculation, two parameters should be added to the NAMD configuration file must set (three when restarting a previous run):

Output files

By default, the collective variables module writes three output files:

Other output files may be written by specific methods applied to the colvars (e.g. by the ABF method, see 10.3.1, or the metadynamics method, see 10.3.2). Like the colvar trajectory file, they are needed only for analyzing, not continuing a simulation. All such files' names also begin with the prefix $ <$outputName$ >$.

Colvars module configuration file

Except for the three NAMD keywords listed above (colvars, colvarsConfig and colvarsInput), all the parameters defining the colvars and their biases are read from the extra input file (provided by colvarsConfig). Hence, none of the keywords described in this and the following sections are available in the NAMD main configuration.

The syntax of the collective variables configuration file is similar to that of the NAMD file (2.2.1), with a few important differences:

Three global options are available:

The following is a typical configuration file. The options available inside the two colvar blocks are documented in 10.2. harmonic defines an harmonic potential, which is one of the available biases, documented in 10.3. Note: except colvar, none of the keywords below is mandatory.

# collective variables config file: two distances

colvarsTrajFrequency 100 # output values every 100 steps

colvar {
  name 1st-colvar # needed to identify the variable

  outputSystemForce yes # report also the system force on this colvar
                        # (in addition to the current value)
  distance {
    group1 {
      atomNumbers 1 2 3 
    group2 {
      atomNumbers 4 5 6 

colvar {
  name 2nd-colvar

harmonic {
  name my_pot
  colvars 1st-colvar 2nd-colvar
  centers 3.0 4.0
  forceConstant 5.0

In the following, the section 10.2 explains how to define a colvar. 10.2.2 lists the available colvar components; 10.2.3 defines how to combine existing components to create new types of colvars; 10.2.4 documents how to define in a compact way atom groups, which are used by most components; 10.2.5 lists the available option for runtime statistical analysis of the colvars.

10.3 lists the available methods to perform biased simulations and multidimensional analysis (ABF, harmonic restraint, histogram, and metadynamics).

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