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Subsections


General parameters and input/output files

To enable a collective variable calculation, one or more parameters are added to the NAMD configuration file. In 10.1.1, we document the syntax of such parameters. One of these is the name of a configuration file for the collective variables module itself, which is described in 10.1.2, and in the following sections.


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 file 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 file is ``keyword value'', where the keyword and its value are separated by any white space. The following rules apply:

All parameters defining the colvars and their biasing or analysis algorithms are read from the file specified by colvarsConfig. The following keywords are available in the global context of this configuration file, i.e. 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 configuration file, an optional input state file may be provided to continue a previous simulation. The name of this file is provided as a value to the keyword colvarsInput.


Output files

In addition to the output files written by NAMD, 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.


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