Global keywords

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

• colvarsTrajFrequency $\langle\,$ Colvar value trajectory frequency$\,\rangle$
  Context: global
  Acceptable values: positive integer
  Default value: 100
  Description: The values of each colvar (and of other related quantities, if requested) are written to the file outputName.colvars.traj every these many steps throughout the simulation. If the value is 0, such trajectory file is not written. For optimization the output is buffered, and synchronized with the disk only when the restart file is being written.

• colvarsRestartFrequency $\langle\,$ Colvar module restart frequency$\,\rangle$
  Context: global
  Acceptable values: positive integer
  Default value:
  Description: The state file and any other output files produced by Colvars are written every these many steps (the trajectory file is still written every colvarsTrajFrequency steps). In VMD, the simulation step is not progressed and this parameter is effectively ignored. It is generally a good idea to leave this parameter at its default value, unless needed for special cases or to disable automatic writing of output files altogether. Writing can still be invoked at any time via the command cv save.

• indexFile $\langle\,$ Index file for atom selection (GROMACS ``ndx'' format)$\,\rangle$
  Context: global
  Acceptable values: UNIX filename
  Description: This option reads an index file (usually with a .ndx extension) as produced by the make_ndx tool of GROMACS. This keyword may be repeated to load multiple index files. A group with the same name may appear multiple times, as long as it contains the same indices in identical order each time: an error is raised otherwise. The names of index groups contained in this file can then be used to define atom groups with the indexGroup keyword. Other supported methods to select atoms are described in .

• smp $\langle\,$ Whether SMP parallelism should be used$\,\rangle$
  Context: global
  Acceptable values: boolean
  Default value: on
  Description: If this flag is enabled (default), SMP parallelism over threads will be used to compute variables and biases, provided that this is supported by the VMD build in use.

To illustrate the flexibility of the Colvars module, a non-trivial setup is represented in Figure 13.1. The corresponding configuration is given below. The options within the colvar blocks are described in , those within the harmonic and histogram blocks in . Note: except colvar, none of the keywords shown is mandatory.

Figure 13.1: Graphical representation of a Colvars configuration. The colvar called ``$d$ '' is defined as the difference between two distances: the first distance ($d_{1}$ ) is taken between the center of mass of atoms 1 and 2 and that of atoms 3 to 5, the second ($d_{2}$ ) between atom 7 and the center of mass of atoms 8 to 10. The difference $d = d_{1} - d_{2}$ is obtained by multiplying the two by a coefficient $C = +1$ or $C = -1$ , respectively. The colvar called ``$c$ '' is the coordination number calculated between atoms 1 to 10 and atoms 11 to 20. A harmonic restraint is applied to both $d$ and $c$ : to allow using the same force constant $K$ , both $d$ and $c$ are scaled by their respective fluctuation widths $w_d$ and $w_c$ . A third colvar ``alpha'' is defined as the $\alpha$ -helical content of residues 1 to 10. The values of ``$c$ '' and ``alpha'' are also recorded throughout the simulation as a joint 2-dimensional histogram.

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 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 documents how to select atoms, and section lists all of the available functional forms, which we call ``colvar components''. Finally, section lists the available methods and algorithms to perform biased simulations and multidimensional analysis of colvars.