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Collective Variable-based Calculations1

The features described in this section were contributed by Giacomo Fiorin and Jérôme Hénin, Center for Molecular Modeling, University of Pennsylvania.

The collective variables module replaces and greatly extends the functionality of the older freeEnergy module for free energy of conformational change calculations. The older module is still available in the code, but has been removed from the documentation to discourage future use.

Today's molecular dynamics simulations involve a large number of degrees of freedom (typically 10,000-1,000,000), and it is often useful to reduce the description to a few parameters which can be either analyzed individually, or manipulated in order to alter the dynamics of the system in a controlled manner. Such reduced degrees of freedom have been called `order parameters', `collective variables', `(surrogate) reaction coordinates', and many other terms. In this section, the term `collective variable' (shortened to colvar) is used, and it indicates any differentiable function of atomic Cartesian coordinates, $ {\mbox{\boldmath {$x$}}}_{i}$, with $ i$ between $ 1$ and $ N$, the total number of atoms:

$\displaystyle \xi(t) \; = \xi\left({\mbox{\boldmath {$x$}}}_{i}(t), {\mbox{\bol...
...mbox{\boldmath {$x$}}}_{k}(t), \ldots \right)\;, \;\; 1 \leq i,j,k\ldots \leq N$ (11)

The collective variables module in NAMD offers a mechanism to define several collective variables, and execute various tasks on them. Its most important features are:



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