Documentation

Below you can find the repository of the most commonly used parameters (and their descriptions) in MOSAICS. Note, that not all options are necessary to perform a calculation (simulation) with MOSAICS. Some examples and tutorials on this website use the minimal number of options necessary for a given application. Therefore, it is recommended to study those applications in combination with the brief description of different options here. Each parameter can be defined by using the syntax, \parameter{x}, where x the value chosen for the parameter. In the below descriptions \parameter{a} indicates that parameter has the default value a, otherwise parameter is listed as \parameter{ }. In each case the argument type is explained. To specify parameter options for performing a computation of a given system with MOSAICS one has to define sets of parameters:

Simulation parameters

Defines parameters that are independent of the given system of interest. For example, performing parallel tempering Monte Carlo can be done for any system and the implementation of the parallel tempering MCMC is independent of the choice of the system.
To view this set of parameters click on simulation parameters.

System parameters

These parameters define the model representation, which includes the resolution (e.g. one center per nucleotide or atomistic), and the corresponding interaction potential (e.g. physics based or statistical) describing how atoms (or centers) interact.
To view these parameters click on system parameters.

Header parameters

In the beginning of the .pdb files some parameters may be included to indicate how to treat different chains.
To view these parameters click on header parameters.

Region parameters

This is used for hierarchical sampling and describe/specify how regions and the elements in the region move in a Monte Carlo simulation.
To view these parameters click on region parameters.