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Overview

In molecular dynamics simulations, it is often useful to reduce the large number of degrees of freedom of a physical system into few parameters whose statistical distributions can be analyzed individually, or used to define biasing potentials to alter the dynamics of the system in a controlled manner. These have been called `order parameters', `collective variables', `(surrogate) reaction coordinates', and many other terms.

Here we use primarily the term `collective variable', often shortened to colvar, to indicate any differentiable function of atomic Cartesian coordinates, $ {\mbox{\boldmath {$x$}}}_{i}$ , with $ i$ between $ 1$ and $ N$ , the total number of atoms:

$\displaystyle \xi(t) \; = \xi({\mbox{\boldmath {$X$}}}(t)) \; = \xi\left({\mbox...
...mbox{\boldmath {$x$}}}_{k}(t), \ldots \right)\;, \;\; 1 \leq i,j,k\ldots \leq N$ (35)

The module is designed to perform multiple tasks concurrently during or after a simulation, the most common of which are:

Detailed explanations of the design of the Colvars module are provided in reference [33]. Please cite this reference whenever publishing work that makes use of this module.


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