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:

$$\xi(t) \; = \xi({\mbox{\boldmath {$X$}}}(t)) \; = \xi\left({\mbox... ...mbox{\boldmath {$x$}}}_{k}(t), \ldots \right)\;, \;\; 1 \leq i,j,k\ldots \leq N$$ (13.1)

The Colvars module in VMD may be used to calculate these functions over a molecular structure, and to analyze the results of previous simulations. The module is designed to perform multiple tasks concurrently during or after a simulation, the most common of which are:

• apply restraints or biasing potentials to multiple variables, tailored on the system by choosing from a wide set of basis functions, without limitations on their number or on the number of atoms involved;

• calculate potentials of mean force (PMFs) along any set of variables, using different enhanced sampling methods, such as Adaptive Biasing Force (ABF), metadynamics, steered MD and umbrella sampling; variants of these methods that make use of an ensemble of replicas are supported as well;

• calculate statistical properties of the variables, such as running averages and standard deviations, correlation functions of pairs of variables, and multidimensional histograms: this can be done either at run-time without the need to save very large trajectory files, or after a simulation has been completed using VMD and the cv command.

Note: although restraints and PMF algorithms are primarily used during simulations, they are also available in VMD to test a new input for a simulation, or to evaluate the relative free energy of a new structure based on data from a previous calculation. Options that only have an effect during a simulation are also included for compatibility purposes.

Detailed explanations of the design of the Colvars module are provided in reference [48]. Please cite this reference whenever publishing work that makes use of this module.

Using the Colvars Module in VMD

Within VMD, the Colvars Module can be accessed in two ways:

• Using the Colvars dashboard, an intuitive, but partial interface to the Colvars module, to easily define and analyze collective variables, but not biases (section ).
• Using the full-featured Tcl scripting interface as documented in section ; see in particular the example in section .