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# Collective Variable-based Calculations1

In today's molecular dynamics simulations, it is often useful to reduce the great number of degrees of freedom of a into a few parameters which can be either analyzed individually, or manipulated in order to alter the dynamics in a controlled manner. These 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, , with between and , the total number of atoms:

 (35)

The colvars module in NAMD may be used in both MD simulation and energy minimization runs (except free energy methods). It offers several features:

• define an arbitrary number of colvars, and perform a multidimensional analysis or biased simulation by accessing any subset of colvars independently from the rest (see 10.1);

• combine different functions of Cartesian coordinates (herein termed colvar components) into a colvar defined as a polynomial of several such components, thereby implementing new functional forms at runtime; periodic, multidimensional and symmetric components are handled transparently (see 10.2.2);

• calculate potentials of mean force (PMFs) for any set of colvars, using different sampling methods: currently implemented are the Adaptive Biasing Force (ABF) method (see 10.3.1), metadynamics (see 10.3.2), Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) via a flexible harmonic restraint bias (see 10.3.3);

• calculate statistical properties of the colvars, such as their running averages and standard deviations, time correlation functions, and multidimensional histograms, without the need to save very large trajectory files.

• compute collective variable values from existing coordinates (e.g. an MD trajectory): use NAMD's coorfile read command, and perform a 0-timestep run for each set of coordinates, as illustrated in 16.

Subsections

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