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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,
, with
between
and
, the total number of atoms:
 |
(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:
- defining an arbitrary number of colvars, and perform a
multidimensional analysis or biased simulation by accessing any
subset of colvars independently from the others (see
9.1);
- 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 9.2.1);
- calculate potentials of mean force (PMFs) or free energy
surfaces for any set of colvars, using different sampling methods:
currently implemented are the Adaptive Biasing Force (ABF)
method (see 9.3.1), metadynamics (see
9.3.2), and Steered Molecular Dynamics (SMD)
(see 9.3.3); any number of harmonic
restraints can also be applied to the colvars (see
9.3.3);
- calculate statistical properties of an individual collective
variable along a simulated trajectory, such as its running average,
standard deviation or the time auto-correlation function (ACF)
of its value, its velocity, or its total force (see
9.2.4);
- perform multidimensional correlation analysis, by calculating
frequency histograms of any subset of colvars.
Subsections
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