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Subsections


General parameters and input/output files

The structure of a typical collective variables calculation is depicted in Figure 6. Each colvar is a combination of one or more components (see 9.2), which are functions of several atomic coordinates. Multiple biasing or analysis methods can be applied to the same colvars. But care should be taken that certain methods (such as free energy reconstruction) do not function properly if other biases are adding forces to their colvars.

Figure 6: Example of a collective variables (colvar) configuration. The colvar ``$ d$'' is defined as the difference between two distances, each calculated between the centers of mass of two atom groups. The second colvar ``$ c$'' holds the coordination number (i.e. the number of contacts) within a radius of 6 Å between two groups. The third colvar ``alpha'' measures the degree of $ \alpha $-helicity of the protein segment between residues 1 and 10. A moving harmonic restraint is applied to the colvars ``$ d$'' and ``$ c$'', each rescaled by means of width parameters $ w_{d}$ and $ w_{c}$; the centers of the restraint, $ d_0$ and $ c_0$, evolve with the simulation time $ t$. The histogram of ``alpha'' and ``$ c$'' is also recorded on-the-fly.
\includegraphics[width=12cm]{figures/colvars_diagram}

NAMD parameters

To enable a colvar calculation, the NAMD configuration file must set two parameters (three when restarting a previous run):

Othe parameters defining a collective variables calculation are not read from the NAMD configuration file, but from a separate file. As a consequence, keywords described in the following sections are not NAMD keywords.

Output files

By default, the collective variables module writes three output files:

Other output files can written by specific methods applied to the colvars (e.g. by the ABF method, see 9.3.1, or the metadynamics method, see 9.3.2): as for the colvar trajectory file, they are meant for analyzing rather than continuing a simulation. All such files begin with the prefix $ <$outputName$ >$.

Colvars module configuration file

Figure 7 shows a typical collective variables configuration file. Its syntax is similar to that of the NAMD configuration file (2.2.1), with a few differences:

Figure 7: A typical colvars configuration file
\begin{figure}\footnotesize
\begin{verbatim}...

Options like globalOption define general features of the colvars module, and are described in the following. The options for the colvar blocks are documented in 9.2, and those for the colvar biases' blocks biastype1, biastype2, ...in 9.3.


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