next up previous contents index
Next: Selecting atoms for colvars: Up: Collective Variable-based Calculations1 Previous: General parameters and input/output   Contents   Index

Subsections


Defining collective variables and their properties

In the configuration file each colvar is defined by the keyword colvar, followed by its configuration options within curly braces: colvar { ... }. One of these options is the name of a colvar component: for example, including rmsd { ... } defines the colvar as a RMSD function. In most applications, only one component is used, and the component is equal to the colvar.

The full list of colvar components can be found in Section 10.4, with the syntax to select atoms in Section 10.3. The following section lists several options to control the behavior of a single colvar, regardless of its type.


General options for a collective variable

The following options are not required by default; however, the first four are very frequently used:

Artificial boundary potentials (walls)

The following options are useful to define restraints (confining potentials) for this colvar. To apply moving restraints, or restraints to more than one colvar simultaneously, a more convenient option is to use the harmonic bias (10.5.3). When using an extended Lagrangian, the boundary potential is applied to the ``actual'' colvar, in contrast with forces for all types of biases, which are applied to the extended coordinate.

Trajectory output


Extended Lagrangian.

The following options enable extended-system dynamics, where a colvar is coupled to an additional degree of freedom (fictitious particle) by a harmonic spring. All biasing and confining forces are then applied to the extended degree of freedom. The ``actual'' geometric colvar (function of Cartesian coordinates) only feels the force from the harmonic spring and its wall potentials, if any.


Statistical analysis of collective variables

When the global keyword analysis is defined in the configuration file, run-time calculations of statistical properties for individual colvars can be performed. At the moment, several types of time correlation functions, running averages and running standard deviations are available.


next up previous contents index
Next: Selecting atoms for colvars: Up: Collective Variable-based Calculations1 Previous: General parameters and input/output   Contents   Index
http://www.ks.uiuc.edu/Research/namd/