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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:
 |
(34) |
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 10.2.1);
- 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.
Subsections
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